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Message #11453
[Branch ~yade-pkg/yade/git-trunk] Rev 3448: Merge github.com:yade/trunk into chaoUnsat
Merge authors:
Anton Gladky (gladky-anton)
Anton Gladky (gladky-anton)
Bruno Chareyre (bruno-chareyre)
Christian Jakob (jakob-ifgt)
Dominik Boemer (dominik-boemer)...
------------------------------------------------------------
revno: 3448 [merge]
committer: Chao Yuan <chaoyuan2012@xxxxxxxxx>
timestamp: Thu 2014-09-04 16:50:57 +0200
message:
Merge github.com:yade/trunk into chaoUnsat
removed:
NEWS
py/3rd-party/mtTkinter-0.3/
py/3rd-party/mtTkinter-0.3/mtTkinter.py
added:
doc/sphinx/github.rst
examples/clumps/clump-hopper-test.py
py/3rd-party/mtTkinter-0.4/
py/3rd-party/mtTkinter-0.4/gpl.txt
py/3rd-party/mtTkinter-0.4/lgpl.txt
py/3rd-party/mtTkinter-0.4/mtTkinter.py
scripts/checks-and-tests/checks/checkClumpHopper.py
scripts/checks-and-tests/checks/checkViscElPM.py
modified:
ChangeLog
core/BodyContainer.cpp
doc/references.bib
doc/sphinx/index-toctree.rst
doc/sphinx/installation.rst
doc/sphinx/prog.rst
doc/sphinx/tutorial/06-periodic-triaxial-test.py
pkg/common/ForceEngine.cpp
pkg/common/ForceEngine.hpp
pkg/dem/Shop.hpp
pkg/dem/Shop_02.cpp
pkg/dem/SpherePack.cpp
pkg/dem/TriaxialStressController.cpp
pkg/dem/TriaxialStressController.hpp
pkg/dem/VTKRecorder.cpp
pkg/dem/VTKRecorder.hpp
pkg/dem/ViscoelasticPM.cpp
pkg/pfv/FlowEngine.hpp.in
py/3rd-party/README
py/CMakeLists.txt
py/_utils.cpp
py/pack/_packSpheres.cpp
py/utils.py
scripts/checks-and-tests/checks/DEM-PFV-check.py
scripts/checks-and-tests/checks/checkViscElEng.py
--
lp:yade
https://code.launchpad.net/~yade-pkg/yade/git-trunk
Your team Yade developers is subscribed to branch lp:yade.
To unsubscribe from this branch go to https://code.launchpad.net/~yade-pkg/yade/git-trunk/+edit-subscription
=== modified file 'ChangeLog'
--- ChangeLog 2014-06-25 17:41:03 +0000
+++ ChangeLog 2014-08-04 16:55:34 +0000
@@ -1,4 +1,121 @@
==================================================
+yade-1.11.0
+Mon, 4 Aug 2014 18:54:00 +0200
+
+Alexander Eulitz (9):
+ small corrections of messed up indentations
+ another indentation fixed
+ rearranged compilation and installing procedure so that hints for multicore compilation are placed directly after the make command
+ typo fix
+ fixed --cores implementation and improved arg-parse argument documentation.
+ improved doc of betan and betas
+ replacing damping coefficient betan and betas by damping ratio betan and betas
+ rearranged indentation of examplarily folder structure for yade complation
+ Added hint about make errors during compilation when user does not posses root priviledges.
+
+Anton Gladky (58):
+ Delete RELEASE file.
+ Add YADE_PTR_DYN_CAST to define dynamic_cast.
+ Remove all "using namespace std;"
+ Fix compilation with disabled openmp.
+ Roll back last 2 commits.
+ Remove most of "using namespace std;"
+ Replace math.h by cmath in includes.
+ Remove some more "using namespace std;"
+ Remove "using namespace std;" everywhere. Tests are failing.
+ Replace abs by std::abs.
+ Clean up in header inclusions.
+ First stage of C++11 implementing.
+ Add missing header.
+ Remove isIndexable and isFactorable.
+ Use boost::shared_ptr for C++11 as well.
+ Drop Qt3 workaround
+ Enable LBM by default.
+ Enable C++11 by default.
+ Do not consider Eigen3 like a feature.
+ Capitalize feature list.
+ Use double precision for VTKREcorder.
+ Do not use -DTYPEOF, use explicit decltype
+ Move definitions of YADE_PTR_CAST YADE_CAST YADE_PTR_DYN_CAST into Math.hpp
+ Remove -std=c++0x definition for pygts.
+ Join [CohFrict]Mat, Phys and Ip2_.
+ Move Ip2_*_MindlinCapillaryPhys into HertzMindlin
+ Move Ip2_*_CapillaryPhys. into CapillaryPhys.
+ Move Ip2_FrictMat_* into FrictPhys
+ Move all NormalInelastic files into NormalInelasticPM
+ Join all InelastCohFrict files into InelastCohFrictPM.
+ Join all KinemC*Engine.* into KinemC__Engine.*
+ Set C++11 only for CXX-files, not C
+ Update LICENSE file, does not need exception any more
+ Cut off some header inclusions.
+ Disable reusing of removed body ids.
+ Fix compilation.
+ Replace nullptr by reset().
+ Join all Bo1_* into Bo1_Aabb
+ Remove some more .cpp-files.
+ Move many Gl1_* into Gl1_Primitives.
+ Remove some more small cpp-files.
+ Remove some warnings.
+ Remove LBMbody.cpp and LBMlink.cpp.
+ Remove Indexable.cpp
+ Exclude Indexable.cpp from CMakeLists.txt
+ Redirect --test output into stdout
+ Modify slightly description of save-loadVars
+ Change stderr to stdout in greeting message.
+ Update Vaclav`s occupation in sphinx-doc
+ Cut long line in HertzMindlin.hpp
+ Move some YADE_PLUGINS into common.cpp
+ Fix most of compilation warnings.
+ Return false in BubbleMat, if no penetration.
+ Fix and enable DEM-PFV-check.py.
+ Replace L3eom by SCgeom in stl and gts examples.
+ Use global interpreter lock (GIL) in OpenGLRenderer.
+ Update mtTkinter version.
+ Remove NEWS file (outdated).
+
+Bruno Chareyre (9):
+ Revert "Revert "Set minimal required Eigen3 version 3.2.1"" / Thanks Anton for uploading the backport
+ replace abs by std::abs (complement of https://github.com/yade/trunk/commit/1997c194c0aa759cae101a3dd0a559fcf049b29f)
+ +2 conf papers
+ Law2 return bool - fix https://bugs.launchpad.net/yade/+bug/1324190
+ add missing 'return bool' in some Law2's
+ Revert "implement more accurate porosity calculation..." (temporary required in order to revert 915fd94606af6 without conflict)"
+ Revert "fix typos and indents; cut long lines.. - please no formatting commits (+there is nothing wrong in long lines). Please reapply the documentation part."
+ make growParticles fatser for clumps
+ use Shop::growParticles in TriaxialStressController (fix https://bugs.launchpad.net/yade/+bug/1351275)
+
+Christian Jakob (5):
+ fix typos and indents; cut long lines in TriaxialStressController; bit more documentation of stressMask
+ implement more accurate porosity calculation for clumps in TriaxialStressController; inserted updateClumpProperties command in Triax tutorial
+ Merge branch 'master' of github.com:yade/trunk
+ make PFV compatible with clumps (clumps are treated as spheres with equivalent radius - valid for nearly spherical clumps)
+ reapply 9e512fd50083
+
+Francois (1):
+ Simplify the contact detection in Ig2_GridConnection_GridConnection_GridCoGridCoGeom.
+
+Jan Stransky (3):
+ fixed bug in export.VTKExporter.exportInteractions (question #250922)
+ modification of utils.UnstructuredMesh, added utils.polyhedron
+ fixed bug in MASK_ARBITRARY feature
+
+Jerome Duriez (7):
+ Correction of some broken sphinx links: yade._utils => yade.utils
+ Removal of a double :
+ Improvement of previous commit: there was no extra : but a missing blank line
+ Export principal stresses and directions in VTKRecorder
+ Some shortening in VTKRecorder, mainly according to http://www.mail-archive.com/yade-dev@xxxxxxxxxxxxxxxxxxx/msg10370.html
+ Revert sign convention in bstresses in VTKRecorder (tension=positiv now)
+ Slight modif in JCFpm doc. To better describe the logic of the code.
+
+Kubeu (1):
+ replaced "root" from last commit
+
+Nolan Dyck (2):
+ Update BubbleMat.hpp and BubbleMat.cpp
+ Update bubble example script.
+
+==================================================
yade-1.10.0
Wed, 25 Jun 2014 19:35:00 +0200
=== removed file 'NEWS'
--- NEWS 2011-10-23 14:16:33 +0000
+++ NEWS 1970-01-01 00:00:00 +0000
@@ -1,198 +0,0 @@
-vim:syntax=changelog
-
-2011-10-23 Anton Gladky <gladky.anton@xxxxxxxxx> revision around bzr2942
-
- * RELEASE 0.70.0, Bug-fix release.
-
- * some changes since 0.6
- - Added HarmonicMotionEngine, WirePM
- - Added check-tests to detect regressions
- - A lot of fixes in the code and documentation.
-
-2010-12-01 Václav Šmilauer <eu@xxxxxxxx> revision around bzr bzr2540
-
- * RELEASE 0.6:
- - https://launchpad.net/yade/trunk/0.60
-
- * major changes since 0.5:
- - use boost::serialization (faster, more reliable), use eigen instead of Wm3 (better supported, more flexible)
- - qt4-based interface with on-the-fly inspection and editing of all internal variables
- - support compilation with clang++
- - live plots
- - periodic boundary conditions are much better tested now
- - batch web interface substantially enhanced (including plots, logs, ...)
- - extended attribute flags (readonly, noSave, hidden, ...)
- - added --rebuild, --debug and --test options
-
-2010-04-20 Václav Šmilauer <eudoxos@xxxxxxxx> revision around bzr2150
-
- * RELEASE: 0.5
- - https://launchpad.net/yade/+milestone/0.5
-
- * overall:
- - yade main is now a python script, the c++ part is imported
- - many classes renamed for the sake of consistency, while mostly keeping backward compatibility for scripts
- - all classes (deriving from Serializable) are automatically exposed in python via automatically constructed wrappers, with full attribute access (https://bugs.launchpad.net/yade/+bug/544857)
- - lot of old code removed (to be found in attic/)
-
- * functionality:
- - separated State and (possibly shared) Material for bodies
- - InsertionSortCollider handles both periodic and aperiodic simulations now
- - Cell can undergo arbitrary linear transformation during simulation
- - VTKRecorder saves to VTK-compatible XML files; allows one to use Paraview for post-processing
- - NewtonIntegrator features integration of rotation of non-spherical bodies
- - callback functionality for interaction and body loop (InteractionDispatchers and NewtonIntegrator) (not yet fully done)
- - body and interaction containers devirtualized (https://blueprints.launchpad.net/yade/+spec/devirtualize-containers)
-
- * documentation:
- - New website https://www.yade-dem.org
- - Sphinx documentation https://www.yade-dem.org/sphinx/, containing both hand-written and automatically generated documentation
- - All classes and attributes visible from python are documented now
- - Drop doxygen documentation
-
-
-2009-08-31 Václav Šmilauer <eudoxos@xxxxxxxx> revision around bzr1740
-
- * RELEASE: 0.20.0
-
- * overall:
- - fix many crashers, including synchronization with openGL, GUI and python
- - generate documentation for both python and c++ classes/functions automatically (http://yade.wikia.com/wiki/Reference_documentation)
- - move away from SVN repository at berlios.de to bzr at http://www.launchpad.net/yade; bug tracking and other launchpad features are being used; mailing lists migrated to launchpad
-
- * functionality enhancements (apart from performance-oriented changes):
- - Facets (arbitrary triangulation elements) interacting with spheres, allowing to triangulate any surface
- - support for GTS-compatible triangulated surfaces both as predicates and facet-triangulated simulation elements
- - non-incremental sphere-sphere and sphere-facet contact geometry classes (Dem3DofGeom)
- - ConstitutiveLawDispatcher, for having multiple constitutive laws operating on different interactions
- - schedule to run multiple jobs at time, with different parameters (yade-multi, http://yade.wikia.com/wiki/ScriptParametricStudy)
- - added PhysicalParameters::blockedDOFs
- - periodic boundary conditions
- - interaction logic cleaned up
- - sphere packing generators (orthogonal, hexagonal, loose random, triaxially compacted; periodic coming soon)
- - geometry predicates to clip packing, including boolean operations on predicates
- - infrastructure for regression tests
-
- * performance:
- - consistent openMP support throughout the code (InteractionDispatchers, NewtonsDampedLaw, BexContainer) (http://yade.wikia.com/wiki/Performance_Tuning#openMP)
- - InsertionSortCollider (PersistentSAPCollide removed) (http://yade.wikia.com/wiki/Colliders_performace)
- - InteractionDispatchers that reduce number of loops over interactions to one (http://yade.wikia.com/wiki/Performance_Tuning#InteractionDispatchers)
- - new fast container for interactions (InteractionVecMap) (http://yade.wikia.com/wiki/Performance_Tuning#Containers)
- - caching dispatchers, avoiding repetitive multivirtual call resolution (http://yade.wikia.com/wiki/Performance_Tuning#Dispatcher_cache)
- - runtime profiling information (http://yade.wikia.com/wiki/Speed_profiling_using_TimingInfo_and_TimingDeltas_classes)
- - avoid running collision detection at every step (http://yade.wikia.com/wiki/Insertion_Sort_Collider_Stride)
- - vector and quaternion classes are wrapped in python automatically (faster, avoids hand-written wrappers)
- - removed many python proxy classes, resulting in big speedup of python (e.g. 40 × for some operations)
-
- * building:
- - yade can be optionally with one single plugin containing all packages. Speeds up full compilation considerably and reduces binary size several times.
- - files in pkg/* are picked up automatically by the build system, including linking flags
- - do not install headers, only plugins
- - fix debian-package builds and document the procedure (http://yade.wikia.com/wiki/DebianPackages), special package for docs
- - fix all (or most) compile-time warnings
- - create new top-level py/ directory for python
-
- * python:
- - use natural syntax for class instance construction with attributes
- - run telnet server to make yade accessible while running (from localhost only)
- - save any python variables within the XML file, which will be resurrected next time (utils.saveVars, utils.loadVars)
- - support saving simulation to memory temporarily
- - functions from creating video from simulation (via snapshots, either during simulation or in the player)
-
- * Documentation:
- - Structurized content added http://yade.wikia.com/wiki/Structurized_content
- - FAQ start to implement http://yade.wikia.com/wiki/FAQ
-
-
-2008-08-20 Janek Kozicki <cosurgi@xxxxxxxxx> revision 1579
-
- * RELEASE: 0.12.1
-
- - several python interface improvements
- - add code for plotting histogram of interaction directions
- - added buttons for looking from different directions
- - new contact algorithm for facets
- - added python script for making videos
- - added a TCP server on port 9000 with python console in it
- - new dependency on python-numpy package, which allows faster math in python
- - added a script for parametric studies
-
-
-2008-08-20 Janek Kozicki <cosurgi@xxxxxxxxx> revision 1486
-
- * RELEASE: 0.12
-
- * User interface:
-
- - Refactored Qt3 interface: MDI with simulation running
- asynchronously, with python console
-
- - Python wrapper and console with the ability to control most
- simulation aspects (including creating simulations,
- modifying, inspecting, running, recording data), some parts
- of the UI (setting view, configuring renderer); see
- scripts/simple-scene.py to get started
- (http://yade.wikia.com/wiki/SimpleSceneTutorial)
-
- - Much enhanced simulation recorder and player, saving
- optionally to a single file (sqlite database), the ability to
- create video from simulation with one command (may be done
- offscreen as well): scripts/simple-scene-player.py,
- http://yade.wikia.com/wiki/New:Making_videos
-
- * Graphical Viewer:
-
- - up to 3 clipping planes in the GLViewer, can be manipulated,
- bound to each other, activated/deactivated
-
- - saving view to view configurations inside MetaBody (Alt+7 --
- Alt+9), can be loaded later (from python as well)
-
- - displacement and rotation scaling in GLViewer, using
- PhysicalParameters::refSe3
-
- * Simulation features:
-
- - New moment rotation law, fully tested and working
-
- - All simulation aspects (dt, iteration, virtual time) are now
- inside MetaBody, i.e. are restored exactly as they were from
- .xml
-
- - Much improved triaxial test
-
- - Lattice model can now simulate concrete with steel fibres
-
- * New, experimental features:
-
- - Selectively block any of 6 DOFs ( translation and rotation)
- for individual bodies (PhysicalParameters::blockedDOFs - not
- documented, not conveniently accessible from python
- yet)
-
- - Plotting interface based on pylab see example in
- scripts/simple-scene-graph.py
-
- - Sega's facets and vertices with stl import (for example
- import shapes from blender)
-
- * Serialization:
-
- - Transparent support for compressed .xml.gz and .xml.bz2
- files; dropped support for binary format
-
- - The (de)serializer now (un)escapes all control characters,
- using the &charname; format, arbitrary string values can be
- de/serialized now, including parentheses, quotations marks,
- newlines, tabs, <>.
-
- * Compilation / Development:
-
- - Compilation profiles allow separate option sets for scons;
- simultaneous compilation of multiple profiles is supported
- via the profile=a,b,c
-
- - QGLViewer source is now in our tree, no need to install it
- separately
-
-
=== modified file 'core/BodyContainer.cpp'
--- core/BodyContainer.cpp 2014-07-17 08:05:16 +0000
+++ core/BodyContainer.cpp 2014-09-01 09:53:04 +0000
@@ -29,34 +29,35 @@
bool BodyContainer::erase(Body::id_t id, bool eraseClumpMembers){//default is false (as before)
if(!body[id]) return false;
-
const shared_ptr<Body>& b=Body::byId(id);
-
if ((b) and (b->isClumpMember())) {
- const shared_ptr<Body>& clumpBody=Body::byId(b->clumpId);
+ const shared_ptr<Body> clumpBody=Body::byId(b->clumpId);
const shared_ptr<Clump> clump=YADE_PTR_CAST<Clump>(clumpBody->shape);
Clump::del(clumpBody, b);
-
- if (clump->members.size()==0) this->erase(b->clumpId,false); //Clump has no members any more. Remove it
+ if (clump->members.size()==0) this->erase(clumpBody->id,false); //Clump has no members any more. Remove it
}
if ((b) and (b->isClump())){
//erase all members if eraseClumpMembers is true:
const shared_ptr<Clump>& clump=YADE_PTR_CAST<Clump>(b->shape);
std::map<Body::id_t,Se3r>& members = clump->members;
- FOREACH(MemberMap::value_type& mm, members){
- const Body::id_t& memberId=mm.first;
- if (eraseClumpMembers) this->erase(memberId,false); // erase members
- //when the last members is erased, the clump will be erased automatically, see above
- else Body::byId(memberId)->clumpId=Body::id_t(-1); // make members standalones
+ std::vector<Body::id_t> idsToRemove;
+ FOREACH(MemberMap::value_type mm, members) idsToRemove.push_back(mm.first); // Prepare an array of ids, which need to be removed.
+ FOREACH(Body::id_t memberId, idsToRemove){
+ if (eraseClumpMembers) {
+ this->erase(memberId,false); // erase members
+ } else {
+ //when the last members is erased, the clump will be erased automatically, see above
+ Body::byId(memberId)->clumpId=Body::ID_NONE; // make members standalones
+ }
}
+ body[id].reset();
+ return true;
}
const shared_ptr<Scene>& scene=Omega::instance().getScene();
for(Body::MapId2IntrT::iterator it=b->intrs.begin(),end=b->intrs.end(); it!=end; ++it) { //Iterate over all body's interactions
scene->interactions->requestErase((*it).second);
}
-
body[id].reset();
-
return true;
}
=== modified file 'doc/references.bib'
--- doc/references.bib 2014-07-28 06:24:36 +0000
+++ doc/references.bib 2014-08-19 13:59:12 +0000
@@ -735,3 +735,50 @@
pages={447-454},
language={English}
}
+
+@article{Richarson1954,
+ author = {Richardson, J. F., and W. N. Zaki},
+ title = {Sedimentation and fluidization: Part i},
+ journal = {Trans. Instn. Chem. Engrs},
+ year = {1954},
+ volume = {32}
+}
+
+@article{RevilBaudard2013,
+ author = {Revil-Baudard, T. and Chauchat, J.},
+ title = {A two-phase model for sheet flow regime based on dense granular flow
+ rheology},
+ journal = {Journal of Geophysical Research: Oceans},
+ year = {2013},
+ volume = {118},
+ pages = {619--634},
+ number = {2}
+}
+
+@article{Schmeeckle2007,
+ author = {Schmeeckle, Mark W. and Nelson, Jonathan M. and Shreve, Ronald L.},
+ title = {Forces on stationary particles in near-bed turbulent flows},
+ journal = {Journal of Geophysical Research: Earth Surface},
+ year = {2007},
+ volume = {112},
+ number = {F2},
+ doi = {10.1029/2006JF000536},
+ url = {http://dx.doi.org/10.1029/2006JF000536}
+}
+
+@article{Wiberg1985,
+ author = {Wiberg, Patricia L. and Smith, J. Dungan},
+ title = {A theoretical model for saltating grains in water},
+ journal = {Journal of Geophysical Research: Oceans},
+ year = {1985},
+ volume = {90},
+ pages = {7341--7354},
+ number = {C4}
+}
+@book{Dallavalle1948,
+ title = {Micrometrics : The technology of fine particles},
+ publisher = {Pitman Pub. Corp},
+ year = {1948},
+ author = {J. M. DallaValle},
+ volume = {2nd edition}
+}
=== added file 'doc/sphinx/github.rst'
--- doc/sphinx/github.rst 1970-01-01 00:00:00 +0000
+++ doc/sphinx/github.rst 2014-08-18 15:34:10 +0000
@@ -0,0 +1,202 @@
+.. _yade-github-label:
+
+##############
+Yade on GitHub
+##############
+
+************************************************
+Fast checkout without GitHub account (read-only)
+************************************************
+
+Getting the source code without registering on GitHub can be done via a single command. It will not allow interactions with the remote repository, which you access the read-only way::
+
+ git clone https://github.com/yade/trunk.git
+
+***************************************************************************
+Using branches on GitHub (for frequent commits see git/trunk section below)
+***************************************************************************
+
+Most usefull commands are below. For more details, see for instance http://gitref.org/index.html and https://help.github.com/articles/set-up-git
+
+Setup
+=====
+
+1. Register on github.com
+
+2. Add your `SSH key <https://help.github.com/articles/generating-ssh-keys>`_ to GitHub:
+
+ On the GitHub site Click “Account Settings” (top right) > Click “SSH keys” > Click “Add SSH key”
+
+3. Set your username and email through terminal:
+
+ ::
+
+ git config --global user.name "Firstname Lastname"
+ git config --global user.email "your_email@xxxxxxxxxxxxx"
+
+4. `Fork a repo <https://help.github.com/articles/fork-a-repo>`_:
+
+ Click the “Fork” button on the https://github.com/yade/trunk
+
+5. Set Up Your Local Repo through terminal:
+
+ ::
+
+ git clone git@xxxxxxxxxx:username/trunk.git
+
+ This creates a new folder, named trunk, that contains the whole code.
+
+6. Configure remotes
+
+ ::
+
+ cd to/newly/created/folder
+ git remote add upstream git@xxxxxxxxxx:yade/trunk.git
+ git fetch upstream
+
+ Now, your "trunk" folder is linked with the code hosted on github.com. Through appropriate commands explained below, you will be able to update your code to include changes commited by others, or to commit yourself changes that others can get.
+
+Retrieving older Commits
+========================
+
+In case you want to work with, or compile, an older version of Yade which is not tagged, you can create your own (local) branch of the corresponding daily build. Look `here <https://answers.launchpad.net/yade/+question/235867>`_ for details.
+
+Committing and updating
+========================
+
+For those used to other version control systems, note that the commit mechanisms in Git significantly differs from that of `Bazaar <http://bazaar.canonical.com/en/>`_ or `SVN <https://subversion.apache.org/>`_. Therefore, don't expect to find a one-to-one command replacement. In some cases, however, the equivalent bazaar command is indicated below to ease the transition.
+
+Inspecting changes
+------------------
+
+You may start by inspecting your changes with a few commands. For the "diff" command, it is convenient to copy from the output of "status" instead of typing the path to modified files. ::
+
+ git status
+ git diff path/to/modified/file.cpp
+
+Committing changes
+------------------
+
+Then you proceed to commit through terminal::
+
+ git add path/to/new/file.cpp #Version a newly created file: equivalent of "bzr add"
+ git commit path/to/new_or_modified/file.cpp -m'Commit message'`` #Validate a change. It can be done several times after every sufficient change. No equivalent in bzr, it's like commiting to your own local repository
+ git push #Push your changes into GitHub. Equivalent of "bzr commit", except that your are commiting to your own remote branch
+
+Changes will be pushed to your personal "fork", If you have tested your changes and you are ready to push them into the main trunk, just do a "pull request" [5] or create a patch from your commit via::
+
+ git format-patch origin #create patch file in current folder)
+
+and send to the developers maililng list (yade-dev@xxxxxxxxxxxxxxxxxxx) as attachment. In either way, after reviewing your changes they will be added to the main trunk.
+
+When the pull request has been reviewed and accepted, your changes are integrated in the main trunk. Everyone will get them via ``git fetch``.
+
+Updating
+--------
+
+You may want to get changes done by others::
+
+ git fetch upstream #Pull new updates from the upstream to your branch. Eq. of "bzr update", updating the remote branch from the upstream yade/trunk
+ git merge upstream/master #Merge upstream changes into your master-branch (eq. of "bzr update", updating your local repository from the remote branch)
+
+Alternatively, this will do fetch+merge all at once (discouraged if you have uncommited changes)::
+
+ git pull
+
+****************************************************************
+Working directly on git/trunk (recommended for frequent commits)
+****************************************************************
+
+This direct access to trunk will sound more familiar to `bzr <http://bazaar.canonical.com/en/>`_ or `svn <https://subversion.apache.org/>`_ users. It is only possible for members of the git team "developpers". Send an email at yade-dev@xxxxxxxxxxxxxxxxxxx to join this team (don't forget to tell your git account name).
+
+* Get trunk:
+
+ ::
+
+ git clone git@xxxxxxxxxx:yade/trunk.git
+
+ This creates a new folder, named trunk, that contains the whole code.
+
+* Update
+
+ ::
+
+ git pull
+
+* Commit to local repository
+
+ ::
+
+ git commit filename1 filename2 ...
+
+* Push changes to remote trunk
+
+ ::
+
+ git push
+
+ Now, the changes you made are included in the on-line code, and can be get back by every user.
+
+To avoid confusing logs after each commit/pull/push cycle, it is better to setup automatic rebase::
+
+ git config --global branch.autosetuprebase always
+
+Now your file ~/.gitconfig should include:
+
+ [branch]
+ autosetuprebase = always
+
+Check also .git/config file in your local trunk folder (rebase = true):
+
+ [branch "master"]
+ remote = origin
+ merge = refs/heads/master
+ rebase = true
+
+Auto-rebase may have unpleasant side effects by blocking "pull" if you have uncommited changes. In this case you can use "git stash"::
+
+ git pull
+ lib/SConscript: needs update
+ refusing to pull with rebase: your working tree is not up-to-date
+ git stash #hide the uncommited changes away
+ git pull #now it's ok
+ git push #push the commited changes
+ git stash pop #get uncommited changes back
+
+********************************************
+General guidelines for pushing to yade/trunk
+********************************************
+
+1. Set autorebase once on the computer! (see above)
+
+2. Inspect the diff to make sure you will not commit junk code (typically some "cout<<" left here and there), using in terminal:
+
+ ::
+
+ git diff file1
+
+ Or, alternatively, any GUI for git: gitg, git-cola...
+
+3. Commit selectively:
+
+ ::
+
+ git commit file1 file2 file3 -m "message" # is good
+ git commit -a -m "message" # is bad. It is the best way to commit things that should not be commited
+
+4. Be sure to work with an up-to-date version launching:
+
+ ::
+
+ git pull
+
+5. Make sure it compiles and that regression tests pass: try "yade --test" and "yade --check".
+
+6. You can finally let all Yade-users enjoy your work:
+
+ ::
+
+ git push
+
+
+**Thanks a lot for your cooperation to Yade!**
=== modified file 'doc/sphinx/index-toctree.rst'
--- doc/sphinx/index-toctree.rst 2013-03-21 19:28:57 +0000
+++ doc/sphinx/index-toctree.rst 2014-08-18 15:34:10 +0000
@@ -29,6 +29,8 @@
installation.rst
+ github.rst
+
formulation.rst
yade.wrapper.rst
=== modified file 'doc/sphinx/installation.rst'
--- doc/sphinx/installation.rst 2014-07-25 08:01:21 +0000
+++ doc/sphinx/installation.rst 2014-08-18 15:34:10 +0000
@@ -90,8 +90,7 @@
git clone git@xxxxxxxxxx:yade/trunk.git
-will download the whole code repository of ``trunk``. Check out `Yade on github
-<https://www.yade-dem.org/wiki/Yade_on_github>`_ wiki page for more.
+will download the whole code repository of ``trunk``. Check out :ref:`yade-github-label` for more.
Alternatively, a read-only checkout is possible via https without a GitHub account (easier if you don't want to modify the main Yade branch)::
=== modified file 'doc/sphinx/prog.rst'
--- doc/sphinx/prog.rst 2014-05-27 11:24:16 +0000
+++ doc/sphinx/prog.rst 2014-08-21 08:51:47 +0000
@@ -106,7 +106,7 @@
which is used for source code, bug tracking, planning, package downloads and more.
The versioning software used is `GIT <http://git-scm.com/>`__, for which a short
-tutorial can be found in a `Yade's wiki pages <https://www.yade-dem.org/wiki/Yade_on_github>`__.
+tutorial can be found in :ref:`yade-github-label`.
GIT is a distributed revision control system. It is available packaged for all major linux distributions.
The source code is hosted on `GitHub <https://github.com/yade/>`__ , which is periodically
=== modified file 'doc/sphinx/tutorial/06-periodic-triaxial-test.py'
--- doc/sphinx/tutorial/06-periodic-triaxial-test.py 2013-03-08 15:05:59 +0000
+++ doc/sphinx/tutorial/06-periodic-triaxial-test.py 2014-09-03 15:59:54 +0000
@@ -35,10 +35,6 @@
if 0:
## uniform distribution
sp.makeCloud((0,0,0),(2,2,2),rMean=.1,rRelFuzz=.3,periodic=True)
-elif 0:
- ## per-fraction distribution
- ## passing: cummulative percentage
- sp.particleSD2(radii=[.09,.1,.2],passing=[40,80,100],periodic=True,numSph=1000)
else:
## create packing from clumps
# configuration of one clump
=== added file 'examples/clumps/clump-hopper-test.py'
--- examples/clumps/clump-hopper-test.py 1970-01-01 00:00:00 +0000
+++ examples/clumps/clump-hopper-test.py 2014-08-12 19:46:58 +0000
@@ -0,0 +1,79 @@
+# -*- coding: utf-8
+
+from yade import pack,export,qt,geom
+import itertools
+from numpy import *
+
+
+kinEnergyMax = 100000
+# Parameters
+tc=0.001# collision time
+en=.3 # normal restitution coefficient
+es=.3 # tangential restitution coefficient
+frictionAngle=radians(35)#
+density=2700
+# facets material
+facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es))
+# default spheres material
+dfltSpheresMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es))
+
+O.dt=.05*tc # time step
+
+Rs=0.05 # particle radius
+
+# Create geometry
+
+x0=0.; y0=0.; z0=0.; ab=.7; at=2.; h=1.; hl=h; al=at*3
+
+zb=z0; x0b=x0-ab/2.; y0b=y0-ab/2.; x1b=x0+ab/2.; y1b=y0+ab/2.
+zt=z0+h; x0t=x0-at/2.; y0t=y0-at/2.; x1t=x0+at/2.; y1t=y0+at/2.
+zl=z0-hl;x0l=x0-al/2.; y0l=y0-al/2.; x1l=x0+al/2.; y1l=y0+al/2.
+
+vibrationPlate = O.bodies.append(geom.facetBunker((x0,y0,z0),
+ dBunker=ab*4.0,dOutput=ab*1.7,hBunker=ab*3,hOutput=ab,hPipe=ab/3.0,
+ wallMask=4,segmentsNumber=10,material=facetMat))
+
+# Create engines
+O.engines=[
+ ForceResetter(),
+ InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),
+ InteractionLoop(
+ [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()],
+ [Ip2_ViscElMat_ViscElMat_ViscElPhys()],
+ [Law2_ScGeom_ViscElPhys_Basic()],
+ ),
+ DomainLimiter(lo=(-4,-4,-1),hi=(4,4,4),iterPeriod=5000,label='domLim'),
+ NewtonIntegrator(damping=0, gravity=[0,0,-9.81]),
+ PyRunner(iterPeriod=6500,command='addBodies()',nDo=7,label='addb'),
+ PyRunner(iterPeriod=1000,command='state()',label='state'),
+]
+
+numSphereGen = 0
+def addBodies():
+ global numSphereGen
+ # Create clumps...
+ clumpColor=(0.0, 0.5, 0.5)
+ for k,l in itertools.product(arange(0,10),arange(0,10)):
+ clpId,sphId=O.bodies.appendClumped([sphere(Vector3(x0t+Rs*(k*4+2),y0t+Rs*(l*4+2),i*Rs*2+zt+ab*3),Rs,color=clumpColor,material=dfltSpheresMat) for i in xrange(4)])
+ numSphereGen += len(sphId)
+
+ # ... and spheres
+ spheresColor=(0.4, 0.4, 0.4)
+ for k,l in itertools.product(arange(0,9),arange(0,9)):
+ sphAloneId=O.bodies.append( [sphere( Vector3(x0t+Rs*(k*4+4),y0t+Rs*(l*4+4),i*Rs*2.3+zt+ab*3),Rs,color=spheresColor,material=dfltSpheresMat) for i in xrange(4) ] )
+ numSphereGen += len(sphAloneId)
+
+def state():
+ global numSphereGen
+ print "Iter %d: Total number of generated spheres %d, removed particles %d, current particles %d, kinEnergy %g"%(O.iter, numSphereGen, domLim.nDeleted, numSphereGen-domLim.nDeleted, utils.kineticEnergy())
+ if (utils.kineticEnergy() > kinEnergyMax):
+ print "Kinetic energy is over a threshold value! Error!"
+
+addBodies()
+
+
+from yade import qt
+qt.View()
+O.saveTmp()
+
+#O.run(50001)
=== modified file 'pkg/common/ForceEngine.cpp'
--- pkg/common/ForceEngine.cpp 2011-04-20 15:52:11 +0000
+++ pkg/common/ForceEngine.cpp 2014-08-19 13:59:12 +0000
@@ -1,6 +1,6 @@
// 2004 © Janek Kozicki <cosurgi@xxxxxxxxxx>
// 2009 © Václav Šmilauer <eudoxos@xxxxxxxx>
-
+// 2014 © Raphael Maurin <raphael.maurin@xxxxxxxxx>
#include"ForceEngine.hpp"
#include<yade/core/Scene.hpp>
@@ -11,7 +11,11 @@
#include<yade/core/IGeom.hpp>
#include<yade/core/IPhys.hpp>
-YADE_PLUGIN((ForceEngine)(InterpolatingDirectedForceEngine)(RadialForceEngine)(DragEngine)(LinearDragEngine));
+#include <boost/random/linear_congruential.hpp>
+#include <boost/random/normal_distribution.hpp>
+#include <boost/random/variate_generator.hpp>
+
+YADE_PLUGIN((ForceEngine)(InterpolatingDirectedForceEngine)(RadialForceEngine)(DragEngine)(LinearDragEngine)(HydroForceEngine));
void ForceEngine::action(){
FOREACH(Body::id_t id, ids){
@@ -77,3 +81,90 @@
}
}
}
+
+void HydroForceEngine::action(){
+ /* Velocity fluctuation determination (not usually done at each dt, that is why it not placed in the other loop) */
+ if (velFluct == true){
+ /* check size */
+ size_t size=vFluct.size();
+ if(size<scene->bodies->size()){
+ size=scene->bodies->size();
+ vFluct.resize(size);
+ }
+ /* reset stored values to zero */
+ memset(& vFluct[0],0,sizeof(Vector2r)*size);
+
+ /* Create a random number generator rnd() with a gaussian distribution of mean 0 and stdev 1.0 */
+ /* see http://www.boost.org/doc/libs/1_55_0/doc/html/boost_random/reference.html and the chapter 7 of Numerical Recipes in C, second edition (1992) for more details */
+ static boost::minstd_rand0 randGen((int)TimingInfo::getNow(true));
+ static boost::normal_distribution<Real> dist(0.0, 1.0);
+ static boost::variate_generator<boost::minstd_rand0&,boost::normal_distribution<Real> > rnd(randGen,dist);
+
+ double rand1 = 0.0;
+ double rand2 = 0.0;
+ /* Attribute a fluid velocity fluctuation to each body above the bed elevation */
+ FOREACH(Body::id_t id, ids){
+ Body* b=Body::byId(id,scene).get();
+ if (!b) continue;
+ if (!(scene->bodies->exists(id))) continue;
+ const Sphere* sphere = dynamic_cast<Sphere*>(b->shape.get());
+ if (sphere){
+ Vector3r posSphere = b->state->pos;//position vector of the sphere
+ int p = floor((posSphere[2]-zRef)/deltaZ); //cell number in which the particle is
+ // if the particle is inside the water and above the bed elevation, so inside the turbulent flow, evaluate a turbulent fluid velocity fluctuation which will be used to apply the drag.
+ if ((p<nCell)&&(posSphere[2]-zRef>bedElevation)) {
+ Real uStar2 = simplifiedReynoldStresses[p];
+ if (uStar2>0.0){
+ Real uStar = sqrt(uStar2);
+ rand1 = rnd();
+ rand2 = -rand1 + rnd();
+ vFluct[id] = Vector2r(rand1*uStar,rand2*uStar);
+ }
+ }
+ }
+
+ }
+ velFluct = false;
+ }
+
+ /* Application of hydrodynamical forces */
+ FOREACH(Body::id_t id, ids){
+ Body* b=Body::byId(id,scene).get();
+ if (!b) continue;
+ if (!(scene->bodies->exists(id))) continue;
+ const Sphere* sphere = dynamic_cast<Sphere*>(b->shape.get());
+ if (sphere){
+ Vector3r posSphere = b->state->pos;//position vector of the sphere
+ int p = floor((posSphere[2]-zRef)/deltaZ); //cell number in which the particle is
+ if ((p<nCell)&&(p>0)) {
+ Vector3r liftForce = Vector3r::Zero();
+ Vector3r dragForce = Vector3r::Zero();
+ Vector2r fluctVelBody = vFluct[id];//fluid velocity fluctuation associated to the particle's position considered.
+ Vector3r vFluid(vxFluid[p]+fluctVelBody.x(),0.0,fluctVelBody.y()); //fluid velocity at the particle's position
+ Vector3r vPart = b->state->vel;//particle velocity
+ Vector3r vRel = vFluid - vPart;//fluid-particle relative velocity
+
+ //Drag force calculation
+ Real Rep = vRel.norm()*sphere->radius*2*rhoFluid/viscoDyn; //particles reynolds number
+ Real A = sphere->radius*sphere->radius*Mathr::PI; //Crossection of the sphere
+ if (vRel.norm()!=0.0) {
+ Real hindranceF = pow(1-phiPart[p],-expoRZ); //hindrance function
+ Real Cd = (0.44 + 24.4/Rep)*hindranceF; //drag coefficient
+ dragForce = 0.5*rhoFluid*A*Cd*vRel.squaredNorm()*vRel.normalized();
+ }
+ //lift force calculation due to difference of fluid pressure between top and bottom of the particle
+ int intRadius = floor(sphere->radius/deltaZ);
+ if ((p+intRadius<nCell)&&(p-intRadius>0)&&(lift==true)) {
+ Real vRelTop = vxFluid[p+intRadius] - vPart[0]; // relative velocity of the fluid wrt the particle at the top of the particle
+ Real vRelBottom = vxFluid[p-intRadius] - vPart[0]; // same at the bottom
+ liftForce[2] = 0.5*rhoFluid*A*Cl*(vRelTop*vRelTop-vRelBottom*vRelBottom);
+ }
+ //buoyant weight force calculation
+ Vector3r buoyantForce = -4.0/3.0*Mathr::PI*sphere->radius*sphere->radius*sphere->radius*rhoFluid*gravity;
+ //add the hydro forces to the particle
+ scene->forces.addForce(id,dragForce+liftForce+buoyantForce);
+ }
+ }
+ }
+}
+
=== modified file 'pkg/common/ForceEngine.hpp'
--- pkg/common/ForceEngine.hpp 2011-04-20 15:52:11 +0000
+++ pkg/common/ForceEngine.hpp 2014-08-19 13:59:12 +0000
@@ -1,5 +1,6 @@
// 2004 © Janek Kozicki <cosurgi@xxxxxxxxxx>
// 2009 © Václav Šmilauer <eudoxos@xxxxxxxx>
+// 2014 © Raphael Maurin <raphael.maurin@xxxxxxxxx>
#pragma once
@@ -67,3 +68,29 @@
);
};
REGISTER_SERIALIZABLE(LinearDragEngine);
+
+
+class HydroForceEngine: public PartialEngine{
+ private:
+ vector<Vector2r> vFluct;
+ public:
+ virtual void action();
+ YADE_CLASS_BASE_DOC_ATTRS(HydroForceEngine,PartialEngine,"Apply drag and lift due to a fluid flow vector (1D) to each sphere + the buoyant weight.\n The applied drag force reads\n\n.. math:: F_{d}=\\frac{1}{2} C_d A\\rho^f|\\vec{v_f - v}| vec{v_f - v} \n\n where $\\rho$ is the medium density (:yref:`density<HydroForceEngine.rhoFluid>`), $v$ is particle's velocity, $v_f$ is the velocity of the fluid at the particle center, $A$ is particle projected area (disc), $C_d$ is the drag coefficient. The formulation of the drag coefficient depends on the local particle reynolds number and the solid volume fraction. The formulation of the drag is [Dallavalle1948]_ [RevilBaudard2013]_ with a correction of Richardson-Zaki [Richardson1954]_ to take into account the hindrance effect. This law is classical in sediment transport. It is possible to activate a fluctuation of the drag force for each particle which account for the turbulent fluctuation of the fluid velocity (:yref:`velFluct`). The model implemented for the turbulent velocity fluctuation is a simple discrete random walk which takes as input the reynolds stress tensor Re_{xz} in function of the depth and allows to recover the main property of the fluctuations by imposing <u_x'u_z'> (z) = <Re>(z)/rho^f. It requires as input <Re>(z)/rho^f called :yref:`simplifiedReynoldStresses` in the code. \n The formulation of the lift is taken from [Wiberg1985]_ and is such that : \n\n.. math:: F_{L}=\\frac{1}{2} C_L A\\rho^f((v_f - v)^2{top} - (v_f - v)^2{bottom}) \n\n Where the subscript top and bottom means evaluated at the top (respectively the bottom) of the sphere considered. This formulation of the lift account for the difference of pressure at the top and the bottom of the particle inside a turbulent shear flow. As this formulation is controversial when approaching the threshold of motion [Schmeeckle2007]_ it is possible to desactivate it with the variable :yref:`lift`.\n The buoyancy is taken into account through the buoyant weight : \n\n.. math:: F_{buoyancy}= - rho^f V^p g \n\n, where g is the gravity vector along the vertical, and V^p is the volume of the particle.",
+ ((Real,rhoFluid,1000,,"Density of the fluid, by default - density of water"))
+ ((Real,viscoDyn,1e-3,,"Dynamic viscosity of the fluid, by default - viscosity of water"))
+ ((Real,zRef,,,"Position of the reference point which correspond to the first value of the fluid velocity"))
+ ((Real,nCell,,,"Size of the vector of the fluid velocity"))
+ ((Real,deltaZ,,,"width of the discretization cell "))
+ ((Real,expoRZ,3.1,,"Value of the Richardson-Zaki exponent, for the correction due to hindrance"))
+ ((bool,lift,true,,"Option to activate or not the evaluation of the lift"))
+ ((Real,Cl,0.2,,"Value of the lift coefficient taken from [Wiberg1985]_"))
+ ((Vector3r,gravity,,,"Gravity vector (may depend on the slope)."))
+ ((vector<Real>,vxFluid,,,"Discretized streamwise fluid velocity profile in function of the depth"))
+ ((vector<Real>,phiPart,,,"Discretized solid volume fraction profile in function of the depth"))
+ ((bool,velFluct,false,,"If true, activate the determination of turbulent fluid velocity fluctuation at the position of each particle, using a simple discrete random walk model based on the Reynolds stresses :yref:`turbStress<HydroForceEngine.squaredAverageTurbfluct>`"))
+ ((vector<Real>,simplifiedReynoldStresses,,,"Vector of size equal to :yref:`turbStress<HydroForceEngine.nCell>` containing the Reynolds stresses divided by the fluid density in function of the depth. simplifiedReynoldStresses(z) = <u_x'u_z'>(z)^2 "))
+ ((Real,bedElevation,,,"Elevation of the bed above which the fluid flow is turbulent and the particles undergo turbulent velocity fluctuation."))
+ );
+};
+REGISTER_SERIALIZABLE(HydroForceEngine);
+
=== modified file 'pkg/dem/Shop.hpp'
--- pkg/dem/Shop.hpp 2014-08-01 17:25:38 +0000
+++ pkg/dem/Shop.hpp 2014-09-03 17:34:07 +0000
@@ -119,7 +119,7 @@
//! Function to compute overall ("macroscopic") stress.
static Matrix3r getStress(Real volume=0);
- static Matrix3r getCapillaryStress(Real volume=0);
+ static Matrix3r getCapillaryStress(Real volume=0, bool mindlin=false);
static Matrix3r stressTensorOfPeriodicCell() { LOG_WARN("Shop::stressTensorOfPeriodicCelli is DEPRECATED: use getStress instead"); return Shop::getStress(); }
//! Compute overall ("macroscopic") stress of periodic cell, returning 2 tensors
//! (contribution of normal and shear forces)
=== modified file 'pkg/dem/Shop_02.cpp'
--- pkg/dem/Shop_02.cpp 2014-08-01 17:25:38 +0000
+++ pkg/dem/Shop_02.cpp 2014-09-03 17:34:07 +0000
@@ -32,6 +32,7 @@
#include<yade/pkg/dem/ScGeom.hpp>
#include<yade/pkg/dem/FrictPhys.hpp>
+#include<yade/pkg/dem/HertzMindlin.hpp>
#include<yade/pkg/common/Grid.hpp>
@@ -366,7 +367,7 @@
return stressTensor/volume;
}
-Matrix3r Shop::getCapillaryStress(Real volume){
+Matrix3r Shop::getCapillaryStress(Real volume, bool mindlin){
Scene* scene=Omega::instance().getScene().get();
if (volume==0) volume = scene->isPeriodic?scene->cell->hSize.determinant():1;
Matrix3r stressTensor = Matrix3r::Zero();
@@ -375,10 +376,10 @@
if (!I->isReal()) continue;
shared_ptr<Body> b1 = Body::byId(I->getId1(),scene);
shared_ptr<Body> b2 = Body::byId(I->getId2(),scene);
- CapillaryPhys* nsi=YADE_CAST<CapillaryPhys*> ( I->phys.get() );
+ Vector3r fCap = mindlin? YADE_CAST<MindlinCapillaryPhys*> (I->phys.get())->fCap : YADE_CAST<CapillaryPhys*> (I->phys.get())->fCap;
Vector3r branch=b1->state->pos -b2->state->pos;
if (isPeriodic) branch-= scene->cell->hSize*I->cellDist.cast<Real>();
- stressTensor += (nsi->fCap)*branch.transpose();
+ stressTensor += fCap*branch.transpose();
}
return stressTensor/volume;
}
=== modified file 'pkg/dem/SpherePack.cpp'
--- pkg/dem/SpherePack.cpp 2014-07-03 07:16:58 +0000
+++ pkg/dem/SpherePack.cpp 2014-09-03 15:59:54 +0000
@@ -272,156 +272,21 @@
return py::make_tuple(edges,cumm);
}
-/* possible enhacement: proportions parameter, so that the domain is not cube, but box with sides having given proportions */
+
long SpherePack::particleSD2(const vector<Real>& radii, const vector<Real>& passing, int numSph, bool periodic, Real cloudPorosity, int seed){
- typedef Eigen::Matrix<Real,Eigen::Dynamic,Eigen::Dynamic> MatrixXr;
- typedef Eigen::Matrix<Real,Eigen::Dynamic,1> VectorXr;
-
- int dim=radii.size()+1;
- if(passing.size()!=radii.size()) throw std::invalid_argument("SpherePack.particleSD2: radii and passing must have the same length.");
- MatrixXr M=MatrixXr::Zero(dim,dim);
- VectorXr rhs=VectorXr::Zero(dim);
- /*
-
- We know percentages for each fraction (Δpi) and their radii (ri), and want to find
- the number of sphere for each fraction Ni and total solid volume Vs. For each fraction,
- we know that the volume is equal to Ni*(4/3*πri³), which must be equal to Vs*Δpi (Δpi is
- relative solid volume of the i-th fraction).
-
- The last equation says that total number of particles (sum of fractions) is equal to N,
- which is the total number of particles requested by the user.
-
- N1 N2 N3 Vs rhs
-
- 4/3πr₁³ 0 0 -Δp₁ | 0
- 0 4/3πr₂³ 0 -Δp₂ | 0
- 0 0 4/3πr₃³ -Δp₃ | 0
- 1 1 1 0 | N
-
- */
- for(int i=0; i<dim-1; i++){
- M(i,i)=(4/3.)*Mathr::PI*pow(radii[i],3);
- M(i,dim-1)=-(passing[i]-(i>0?passing[i-1]:0))/100.;
- M(dim-1,i)=1;
- }
- rhs[dim-1]=numSph;
- // NumsVs=M^-1*rhs: number of spheres and volume of solids
- VectorXr NumsVs(dim); NumsVs=M.inverse()*rhs;
- Real Vs=NumsVs[dim-1]; // total volume of solids
- Real Vtot=Vs/(1-cloudPorosity); // total volume of cell containing the packing
- Vector3r cellSize=pow(Vtot,1/3.)*Vector3r().Ones(); // for now, assume always cubic sample
- Real rMean=pow(Vs/(numSph*(4/3.)*Mathr::PI),1/3.); // make rMean such that particleSD will compute the right Vs (called a bit confusingly Vtot anyway) inversely
- // cerr<<"Vs="<<Vs<<", Vtot="<<Vtot<<", rMean="<<rMean<<endl;
- // cerr<<"cellSize="<<cellSize<<", rMean="<<rMean<<", numSph="<<numSph<<endl;
- return particleSD(Vector3r::Zero(),cellSize,rMean,periodic,"",numSph,radii,passing,false);
+ //deprecated (https://bugs.launchpad.net/yade/+bug/1024443)
+ LOG_ERROR("particleSD2() has been removed. Please use makeCloud() instead.");
};
-// TODO: header, python wrapper, default params
-
// Discrete particle size distribution
long SpherePack::particleSD(Vector3r mn, Vector3r mx, Real rMean, bool periodic, string name, int numSph, const vector<Real>& radii, const vector<Real>& passing, bool passingIsNotPercentageButCount, int seed){
- vector<Real> numbers;
- if(!passingIsNotPercentageButCount){
- Real Vtot=numSph*4./3.*Mathr::PI*pow(rMean,3.); // total volume of the packing (computed with rMean)
-
- // calculate number of spheres necessary per each radius to match the wanted psd
- // passing has to contain increasing values
- for (size_t i=0; i<radii.size(); i++){
- Real volS=4./3.*Mathr::PI*pow(radii[i],3.);
- if (i==0) {numbers.push_back(passing[i]/100.*Vtot/volS);}
- else {numbers.push_back((passing[i]-passing[i-1])/100.*Vtot/volS);} //
- cout<<"fraction #"<<i<<" ("<<passing[i]<<"%, r="<<radii[i]<<"): "<<numbers[i]<<" spheres, fraction/cloud volumes "<<volS<<"/"<<Vtot<<endl;
- }
- } else {
- FOREACH(Real p, passing) numbers.push_back(p);
- }
-
- static boost::minstd_rand randGen(seed!=0?seed:(int)TimingInfo::getNow(true));
- static boost::variate_generator<boost::minstd_rand&, boost::uniform_real<> > rnd(randGen, boost::uniform_real<>(0,1));
-
- const int maxTry=1000;
- Vector3r size=mx-mn;
- if(periodic)(cellSize=size);
- for (int ii=(int)radii.size()-1; ii>=0; ii--){
- Real r=radii[ii]; // select radius
- for(int i=0; i<numbers[ii]; i++) { // place as many spheres as required by the psd for the selected radius into the free spot
- int t;
- for(t=0; t<maxTry; ++t){
- Vector3r c;
- if(!periodic) { for(int axis=0; axis<3; axis++) c[axis]=mn[axis]+r+(size[axis]-2*r)*rnd(); }
- else { for(int axis=0; axis<3; axis++) c[axis]=mn[axis]+size[axis]*rnd(); }
- size_t packSize=pack.size(); bool overlap=false;
- if(!periodic){
- for(size_t j=0; j<packSize; j++){ if(pow(pack[j].r+r,2) >= (pack[j].c-c).squaredNorm()) { overlap=true; break; } }
- } else {
- for(size_t j=0; j<packSize; j++){
- Vector3r dr;
- for(int axis=0; axis<3; axis++) dr[axis]=min(cellWrapRel(c[axis],pack[j].c[axis],pack[j].c[axis]+size[axis]),cellWrapRel(pack[j].c[axis],c[axis],c[axis]+size[axis]));
- if(pow(pack[j].r+r,2)>= dr.squaredNorm()){ overlap=true; break; }
- }
- }
- if(!overlap) { pack.push_back(Sph(c,r)); break; }
- }
- if (t==maxTry) {
- if(numbers[ii]>0) LOG_WARN("Exceeded "<<maxTry<<" tries to insert non-overlapping sphere to packing. Only "<<i<<" spheres were added, although you requested "<<numbers[ii]<<" with radius "<<radii[ii]);
- return i;
- }
- }
- }
- return pack.size();
+ //deprecated (https://bugs.launchpad.net/yade/+bug/1024443)
+ LOG_ERROR("particleSD() has been removed. Please use makeCloud() instead.");
}
-// 2d function
long SpherePack::particleSD_2d(Vector2r mn, Vector2r mx, Real rMean, bool periodic, string name, int numSph, const vector<Real>& radii, const vector<Real>& passing, bool passingIsNotPercentageButCount, int seed){
- vector<Real> numbers;
- if(!passingIsNotPercentageButCount){
- Real Vtot=numSph*4./3.*Mathr::PI*pow(rMean,3.); // total volume of the packing (computed with rMean)
-
- // calculate number of spheres necessary per each radius to match the wanted psd
- // passing has to contain increasing values
- for (size_t i=0; i<radii.size(); i++){
- Real volS=4./3.*Mathr::PI*pow(radii[i],3.);
- if (i==0) {numbers.push_back(passing[i]/100.*Vtot/volS);}
- else {numbers.push_back((passing[i]-passing[i-1])/100.*Vtot/volS);} //
- cout<<"fraction #"<<i<<" ("<<passing[i]<<"%, r="<<radii[i]<<"): "<<numbers[i]<<" spheres, fraction/cloud volumes "<<volS<<"/"<<Vtot<<endl;
- }
- } else {
- FOREACH(Real p, passing) numbers.push_back(p);
- }
-
- static boost::minstd_rand randGen(seed!=0?seed:(int)TimingInfo::getNow(true));
- static boost::variate_generator<boost::minstd_rand&, boost::uniform_real<> > rnd(randGen, boost::uniform_real<>(0,1));
-
- const int maxTry=1000;
- Vector2r size=mx-mn;
- //if(periodic)(cellSize=size); in this case, it must be defined in py script as cell needs the third dimension
- for (int ii=(int)radii.size()-1; ii>=0; ii--){
- Real r=radii[ii]; // select radius
- for(int i=0; i<numbers[ii]; i++) { // place as many spheres as required by the psd for the selected radius into the free spot
- int t;
- for(t=0; t<maxTry; ++t){
- Vector3r c;
- if(!periodic) { for(int axis=0; axis<2; axis++) c[axis]=mn[axis]+r+(size[axis]-2*r)*rnd(); }
- else { for(int axis=0; axis<2; axis++) c[axis]=mn[axis]+size[axis]*rnd(); }
- size_t packSize=pack.size(); bool overlap=false;
- if(!periodic){
- for(size_t j=0; j<packSize; j++){ if(pow(pack[j].r+r,2) >= (pack[j].c-c).squaredNorm()) { overlap=true; break; } }
- } else {
- for(size_t j=0; j<packSize; j++){
- Vector3r dr=Vector3r::Zero();
- for(int axis=0; axis<2; axis++) dr[axis]=min(cellWrapRel(c[axis],pack[j].c[axis],pack[j].c[axis]+size[axis]),cellWrapRel(pack[j].c[axis],c[axis],c[axis]+size[axis]));
- if(pow(pack[j].r+r,2)>= dr.squaredNorm()){ overlap=true; break; }
- }
- }
- if(!overlap) { pack.push_back(Sph(c,r)); break; }
- }
- if (t==maxTry) {
- if(numbers[ii]>0) LOG_WARN("Exceeded "<<maxTry<<" tries to insert non-overlapping sphere to packing. Only "<<i<<" spheres were added, although you requested "<<numbers[ii]<<" with radius "<<radii[ii]);
- return i;
- }
- }
- }
- return pack.size();
+ //deprecated (https://bugs.launchpad.net/yade/+bug/1024443)
+ LOG_ERROR("particleSD_2d() has been removed. Please use makeCloud() instead.");
}
long SpherePack::makeClumpCloud(const Vector3r& mn, const Vector3r& mx, const vector<shared_ptr<SpherePack> >& _clumps, bool periodic, int num, int seed){
=== modified file 'pkg/dem/TriaxialStressController.cpp'
--- pkg/dem/TriaxialStressController.cpp 2014-08-01 17:27:01 +0000
+++ pkg/dem/TriaxialStressController.cpp 2014-08-13 13:31:41 +0000
@@ -103,7 +103,7 @@
depth = p_front->se3.position.z() - p_back->se3.position.z() - thickness;
boxVolume = height * width * depth;
- if (first) {
+ if ( (first) || (updatePorosity) ) {
BodyContainer::iterator bi = scene->bodies->begin();
BodyContainer::iterator biEnd = scene->bodies->end();
@@ -121,6 +121,7 @@
}
}
first = false;
+ updatePorosity = false;
}
max_vel1=3 * width /(height+width+depth)*max_vel;
max_vel2=3 * height /(height+width+depth)*max_vel;
=== modified file 'pkg/dem/TriaxialStressController.hpp'
--- pkg/dem/TriaxialStressController.hpp 2014-08-01 15:37:51 +0000
+++ pkg/dem/TriaxialStressController.hpp 2014-08-13 13:31:41 +0000
@@ -116,6 +116,7 @@
((Real,meanStress,0,Attr::readonly,"Mean stress in the packing. |yupdate|"))
((Real,volumetricStrain,0,Attr::readonly,"Volumetric strain (see :yref:`TriaxialStressController::strain`).|yupdate|"))
((Real,externalWork,0,Attr::readonly,"Energy provided by boundaries.|yupdate|"))
+ ((bool,updatePorosity,false,,"If true porosity calculation will be updated once (will automatically reset to false after one calculation step). Can be used, when volume of particles changes during the simulation (e.g. when particles are erased or when clumps are created)."))
,
/* deprecated */
((sigma1,goal1,"renamed 'goal1', it can now also be a strain depending on stressMask"))
=== modified file 'pkg/dem/VTKRecorder.cpp'
--- pkg/dem/VTKRecorder.cpp 2014-07-17 08:39:25 +0000
+++ pkg/dem/VTKRecorder.cpp 2014-08-20 13:03:23 +0000
@@ -59,6 +59,7 @@
recActive[REC_CLUMPID]=true;
recActive[REC_MATERIALID]=true;
recActive[REC_STRESS]=true;
+ recActive[REC_FORCE]=true;
if (scene->isPeriodic) { recActive[REC_PERICELL]=true; }
}
else if(rec=="spheres") recActive[REC_SPHERES]=true;
@@ -75,6 +76,7 @@
else if((rec=="clumpids") || (rec=="clumpId")) recActive[REC_CLUMPID]=true;
else if(rec=="materialId") recActive[REC_MATERIALID]=true;
else if(rec=="stress") recActive[REC_STRESS]=true;
+ else if(rec=="force") recActive[REC_FORCE]=true;
else if(rec=="jcfpm") recActive[REC_JCFPM]=true;
else if(rec=="cracks") recActive[REC_CRACKS]=true;
else if(rec=="pericell" && scene->isPeriodic) recActive[REC_PERICELL]=true;
@@ -211,6 +213,22 @@
spheresMaterialId->SetNumberOfComponents(1);
spheresMaterialId->SetName("materialId");
+ vtkSmartPointer<vtkDoubleArray> spheresForceVec = vtkSmartPointer<vtkDoubleArray>::New();
+ spheresForceVec->SetNumberOfComponents(3);
+ spheresForceVec->SetName("forceVec");
+
+ vtkSmartPointer<vtkDoubleArray> spheresForceLen = vtkSmartPointer<vtkDoubleArray>::New();
+ spheresForceLen->SetNumberOfComponents(1);
+ spheresForceLen->SetName("forceLen");
+
+ vtkSmartPointer<vtkDoubleArray> spheresTorqueVec = vtkSmartPointer<vtkDoubleArray>::New();
+ spheresTorqueVec->SetNumberOfComponents(3);
+ spheresTorqueVec->SetName("torqueVec");
+
+ vtkSmartPointer<vtkDoubleArray> spheresTorqueLen = vtkSmartPointer<vtkDoubleArray>::New();
+ spheresTorqueLen->SetNumberOfComponents(1);
+ spheresTorqueLen->SetName("torqueLen");
+
// facets
vtkSmartPointer<vtkPoints> facetsPos = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> facetsCells = vtkSmartPointer<vtkCellArray>::New();
@@ -218,13 +236,13 @@
facetsColors->SetNumberOfComponents(3);
facetsColors->SetName("color");
- vtkSmartPointer<vtkDoubleArray> facetsForceVec = vtkSmartPointer<vtkDoubleArray>::New();
- facetsForceVec->SetNumberOfComponents(3);
- facetsForceVec->SetName("stressVec");
+ vtkSmartPointer<vtkDoubleArray> facetsStressVec = vtkSmartPointer<vtkDoubleArray>::New();
+ facetsStressVec->SetNumberOfComponents(3);
+ facetsStressVec->SetName("stressVec");
- vtkSmartPointer<vtkDoubleArray> facetsForceLen = vtkSmartPointer<vtkDoubleArray>::New();
- facetsForceLen->SetNumberOfComponents(1);
- facetsForceLen->SetName("stressLen");
+ vtkSmartPointer<vtkDoubleArray> facetsStressLen = vtkSmartPointer<vtkDoubleArray>::New();
+ facetsStressLen->SetNumberOfComponents(1);
+ facetsStressLen->SetName("stressLen");
vtkSmartPointer<vtkDoubleArray> facetsMaterialId = vtkSmartPointer<vtkDoubleArray>::New();
facetsMaterialId->SetNumberOfComponents(1);
@@ -234,6 +252,22 @@
facetsMask->SetNumberOfComponents(1);
facetsMask->SetName("mask");
+ vtkSmartPointer<vtkDoubleArray> facetsForceVec = vtkSmartPointer<vtkDoubleArray>::New();
+ facetsForceVec->SetNumberOfComponents(3);
+ facetsForceVec->SetName("forceVec");
+
+ vtkSmartPointer<vtkDoubleArray> facetsForceLen = vtkSmartPointer<vtkDoubleArray>::New();
+ facetsForceLen->SetNumberOfComponents(1);
+ facetsForceLen->SetName("forceLen");
+
+ vtkSmartPointer<vtkDoubleArray> facetsTorqueVec = vtkSmartPointer<vtkDoubleArray>::New();
+ facetsTorqueVec->SetNumberOfComponents(3);
+ facetsTorqueVec->SetName("torqueVec");
+
+ vtkSmartPointer<vtkDoubleArray> facetsTorqueLen = vtkSmartPointer<vtkDoubleArray>::New();
+ facetsTorqueLen->SetNumberOfComponents(1);
+ facetsTorqueLen->SetName("torqueLen");
+
// boxes
vtkSmartPointer<vtkPoints> boxesPos = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> boxesCells = vtkSmartPointer<vtkCellArray>::New();
@@ -241,13 +275,13 @@
boxesColors->SetNumberOfComponents(3);
boxesColors->SetName("color");
- vtkSmartPointer<vtkDoubleArray> boxesForceVec = vtkSmartPointer<vtkDoubleArray>::New();
- boxesForceVec->SetNumberOfComponents(3);
- boxesForceVec->SetName("stressVec");
+ vtkSmartPointer<vtkDoubleArray> boxesStressVec = vtkSmartPointer<vtkDoubleArray>::New();
+ boxesStressVec->SetNumberOfComponents(3);
+ boxesStressVec->SetName("stressVec");
- vtkSmartPointer<vtkDoubleArray> boxesForceLen = vtkSmartPointer<vtkDoubleArray>::New();
- boxesForceLen->SetNumberOfComponents(1);
- boxesForceLen->SetName("stressLen");
+ vtkSmartPointer<vtkDoubleArray> boxesStressLen = vtkSmartPointer<vtkDoubleArray>::New();
+ boxesStressLen->SetNumberOfComponents(1);
+ boxesStressLen->SetName("stressLen");
vtkSmartPointer<vtkDoubleArray> boxesMaterialId = vtkSmartPointer<vtkDoubleArray>::New();
boxesMaterialId->SetNumberOfComponents(1);
@@ -257,6 +291,22 @@
boxesMask->SetNumberOfComponents(1);
boxesMask->SetName("mask");
+ vtkSmartPointer<vtkDoubleArray> boxesForceVec = vtkSmartPointer<vtkDoubleArray>::New();
+ boxesForceVec->SetNumberOfComponents(3);
+ boxesForceVec->SetName("forceVec");
+
+ vtkSmartPointer<vtkDoubleArray> boxesForceLen = vtkSmartPointer<vtkDoubleArray>::New();
+ boxesForceLen->SetNumberOfComponents(1);
+ boxesForceLen->SetName("forceLen");
+
+ vtkSmartPointer<vtkDoubleArray> boxesTorqueVec = vtkSmartPointer<vtkDoubleArray>::New();
+ boxesTorqueVec->SetNumberOfComponents(3);
+ boxesTorqueVec->SetName("torqueVec");
+
+ vtkSmartPointer<vtkDoubleArray> boxesTorqueLen = vtkSmartPointer<vtkDoubleArray>::New();
+ boxesTorqueLen->SetNumberOfComponents(1);
+ boxesTorqueLen->SetName("torqueLen");
+
// interactions
vtkSmartPointer<vtkPoints> intrBodyPos = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> intrCells = vtkSmartPointer<vtkCellArray>::New();
@@ -521,6 +571,19 @@
spheresShearStressVec->InsertNextTupleValue(s);
spheresNormalStressNorm->InsertNextValue(stress.norm());
}
+ if(recActive[REC_FORCE]){
+ scene->forces.sync();
+ const Vector3r& f = scene->forces.getForce(b->getId());
+ const Vector3r& t = scene->forces.getTorque(b->getId());
+ Real ff[3] = { (Real) f[0], (Real) f[1], (Real) f[2] };
+ Real tt[3] = { (Real) t[0], (Real) t[1], (Real) t[2] };
+ Real fn = f.norm();
+ Real tn = t.norm();
+ spheresForceVec->InsertNextTupleValue(ff);
+ spheresForceLen->InsertNextValue(fn);
+ spheresTorqueVec->InsertNextTupleValue(tt);
+ spheresTorqueLen->InsertNextValue(tn);
+ }
if (recActive[REC_CPM]){
cpmDamage->InsertNextValue(YADE_PTR_CAST<CpmState>(b->state)->normDmg);
@@ -574,8 +637,21 @@
if(recActive[REC_STRESS]){
const Vector3r& stress = bodyStates[b->getId()].normStress+bodyStates[b->getId()].shearStress;
Real s[3] = { (Real) stress[0], (Real) stress[1], (Real) stress[2] };
- facetsForceVec->InsertNextTupleValue(s);
- facetsForceLen->InsertNextValue(stress.norm());
+ facetsStressVec->InsertNextTupleValue(s);
+ facetsStressLen->InsertNextValue(stress.norm());
+ }
+ if(recActive[REC_FORCE]){
+ scene->forces.sync();
+ const Vector3r& f = scene->forces.getForce(b->getId());
+ const Vector3r& t = scene->forces.getTorque(b->getId());
+ Real ff[3] = { (Real) f[0], (Real) f[1], (Real) f[2] };
+ Real tt[3] = { (Real) t[0], (Real) t[1], (Real) t[2] };
+ Real fn = f.norm();
+ Real tn = t.norm();
+ facetsForceVec->InsertNextTupleValue(ff);
+ facetsForceLen->InsertNextValue(fn);
+ facetsTorqueVec->InsertNextTupleValue(tt);
+ facetsTorqueLen->InsertNextValue(tn);
}
if (recActive[REC_MATERIALID]) facetsMaterialId->InsertNextValue(b->material->id);
if (recActive[REC_MASK]) facetsMask->InsertNextValue(GET_MASK(b));
@@ -585,6 +661,21 @@
if (recActive[REC_BOXES]){
const Box* box = dynamic_cast<Box*>(b->shape.get());
if (box){
+
+ if(recActive[REC_FORCE]){
+ scene->forces.sync();
+ const Vector3r& f = scene->forces.getForce(b->getId());
+ const Vector3r& t = scene->forces.getTorque(b->getId());
+ Real ff[3] = { (Real) f[0], (Real) f[1], (Real) f[2] };
+ Real tt[3] = { (Real) t[0], (Real) t[1], (Real) t[2] };
+ Real fn = f.norm();
+ Real tn = t.norm();
+ boxesForceVec->InsertNextTupleValue(ff);
+ boxesForceLen->InsertNextValue(fn);
+ boxesTorqueVec->InsertNextTupleValue(tt);
+ boxesTorqueLen->InsertNextValue(tn);
+ }
+
Vector3r pos(scene->isPeriodic ? scene->cell->wrapShearedPt(b->state->pos) : b->state->pos);
Vector3r ext(box->extents);
vtkSmartPointer<vtkQuad> boxes = vtkSmartPointer<vtkQuad>::New();
@@ -626,8 +717,8 @@
if(recActive[REC_STRESS]){
const Vector3r& stress = bodyStates[b->getId()].normStress+bodyStates[b->getId()].shearStress;
Real s[3] = { (Real) stress[0], (Real) stress[1], (Real) stress[2] };
- boxesForceVec->InsertNextTupleValue(s);
- boxesForceLen->InsertNextValue(stress.norm());
+ boxesStressVec->InsertNextTupleValue(s);
+ boxesStressLen->InsertNextValue(stress.norm());
}
if (recActive[REC_MATERIALID]) boxesMaterialId->InsertNextValue(b->material->id);
if (recActive[REC_MASK]) boxesMask->InsertNextValue(GET_MASK(b));
@@ -701,6 +792,12 @@
spheresUg->GetPointData()->AddArray(spheresShearStressVec);
spheresUg->GetPointData()->AddArray(spheresNormalStressNorm);
}
+ if (recActive[REC_FORCE]){
+ spheresUg->GetPointData()->AddArray(spheresForceVec);
+ spheresUg->GetPointData()->AddArray(spheresForceLen);
+ spheresUg->GetPointData()->AddArray(spheresTorqueVec);
+ spheresUg->GetPointData()->AddArray(spheresTorqueLen);
+ }
if (recActive[REC_CPM]){
spheresUg->GetPointData()->AddArray(cpmDamage);
spheresUg->GetPointData()->AddArray(cpmStress);
@@ -743,8 +840,14 @@
facetsUg->SetCells(VTK_TRIANGLE, facetsCells);
if (recActive[REC_COLORS]) facetsUg->GetCellData()->AddArray(facetsColors);
if (recActive[REC_STRESS]){
+ facetsUg->GetCellData()->AddArray(facetsStressVec);
+ facetsUg->GetCellData()->AddArray(facetsStressLen);
+ }
+ if (recActive[REC_FORCE]){
facetsUg->GetCellData()->AddArray(facetsForceVec);
facetsUg->GetCellData()->AddArray(facetsForceLen);
+ facetsUg->GetCellData()->AddArray(facetsTorqueVec);
+ facetsUg->GetCellData()->AddArray(facetsTorqueLen);
}
if (recActive[REC_MATERIALID]) facetsUg->GetCellData()->AddArray(facetsMaterialId);
if (recActive[REC_MASK]) facetsUg->GetCellData()->AddArray(facetsMask);
@@ -771,8 +874,14 @@
boxesUg->SetCells(VTK_QUAD, boxesCells);
if (recActive[REC_COLORS]) boxesUg->GetCellData()->AddArray(boxesColors);
if (recActive[REC_STRESS]){
+ boxesUg->GetCellData()->AddArray(boxesStressVec);
+ boxesUg->GetCellData()->AddArray(boxesStressLen);
+ }
+ if (recActive[REC_FACETS]){
boxesUg->GetCellData()->AddArray(boxesForceVec);
boxesUg->GetCellData()->AddArray(boxesForceLen);
+ boxesUg->GetCellData()->AddArray(boxesTorqueVec);
+ boxesUg->GetCellData()->AddArray(boxesTorqueLen);
}
if (recActive[REC_MATERIALID]) boxesUg->GetCellData()->AddArray(boxesMaterialId);
if (recActive[REC_MASK]) boxesUg->GetCellData()->AddArray(boxesMask);
@@ -881,7 +990,7 @@
crackUg->GetPointData()->AddArray(iter);
crackUg->GetPointData()->AddArray(crackType);
crackUg->GetPointData()->AddArray(crackSize);
- crackUg->GetPointData()->AddArray(crackNorm); //orientation of 2D glyphs does not match this direction (some work to do in order to have the good orientation)
+ crackUg->GetPointData()->AddArray(crackNorm); //see https://www.mail-archive.com/paraview@xxxxxxxxxxxx/msg08166.html to obtain Paraview 2D glyphs conforming to this normal
vtkSmartPointer<vtkXMLUnstructuredGridWriter> writer = vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
if(compress) writer->SetCompressor(compressor);
=== modified file 'pkg/dem/VTKRecorder.hpp'
--- pkg/dem/VTKRecorder.hpp 2014-07-17 08:39:25 +0000
+++ pkg/dem/VTKRecorder.hpp 2014-08-08 09:26:21 +0000
@@ -11,7 +11,7 @@
class VTKRecorder: public PeriodicEngine {
public:
- enum {REC_SPHERES=0,REC_FACETS,REC_BOXES,REC_COLORS,REC_MASS,REC_CPM,REC_INTR,REC_VELOCITY,REC_ID,REC_CLUMPID,REC_SENTINEL,REC_MATERIALID,REC_STRESS,REC_MASK,REC_RPM,REC_JCFPM,REC_CRACKS,REC_WPM,REC_PERICELL,REC_LIQ,REC_BSTRESS};
+ enum {REC_SPHERES=0,REC_FACETS,REC_BOXES,REC_COLORS,REC_MASS,REC_CPM,REC_INTR,REC_VELOCITY,REC_ID,REC_CLUMPID,REC_SENTINEL,REC_MATERIALID,REC_STRESS,REC_MASK,REC_RPM,REC_JCFPM,REC_CRACKS,REC_WPM,REC_PERICELL,REC_LIQ,REC_BSTRESS,REC_FORCE};
virtual void action();
void addWallVTK (vtkSmartPointer<vtkQuad>& boxes, vtkSmartPointer<vtkPoints>& boxesPos, Vector3r& W1, Vector3r& W2, Vector3r& W3, Vector3r& W4);
YADE_CLASS_BASE_DOC_ATTRS_CTOR(VTKRecorder,PeriodicEngine,"Engine recording snapshots of simulation into series of \\*.vtu files, readable by VTK-based postprocessing programs such as Paraview. Both bodies (spheres and facets) and interactions can be recorded, with various vector/scalar quantities that are defined on them.\n\n:yref:`PeriodicEngine.initRun` is initialized to ``True`` automatically.",
@@ -23,7 +23,7 @@
((bool,multiblock,false,,"Use multi-block (``.vtm``) files to store data, rather than separate ``.vtu`` files."))
#endif
((string,fileName,"",,"Base file name; it will be appended with {spheres,intrs,facets}-243100.vtu (unless *multiblock* is ``True``) depending on active recorders and step number (243100 in this case). It can contain slashes, but the directory must exist already."))
- ((vector<string>,recorders,vector<string>(1,string("all")),,"List of active recorders (as strings). ``all`` (the default value) enables all base and generic recorders.\n\n.. admonition:: Base recorders\n\n\tBase recorders save the geometry (unstructured grids) on which other data is defined. They are implicitly activated by many of the other recorders. Each of them creates a new file (or a block, if :yref:`multiblock <VTKRecorder.multiblock>` is set).\n\n\t``spheres``\n\t\tSaves positions and radii (``radii``) of :yref:`spherical<Sphere>` particles.\n\t``facets``\n\t\tSave :yref:`facets<Facet>` positions (vertices).\n\t``boxes``\n\t\tSave :yref:`boxes<Box>` positions (edges).\n\t``intr``\n\t\tStore interactions as lines between nodes at respective particles positions. Additionally stores magnitude of normal (``forceN``) and shear (``absForceT``) forces on interactions (the :yref:`geom<Interaction.geom> must be of type :yref:`NormShearPhys`). \n\n.. admonition:: Generic recorders\n\n\tGeneric recorders do not depend on specific model being used and save commonly useful data.\n\n\t``id``\n\t\tSaves id's (field ``id``) of spheres; active only if ``spheres`` is active.\n\t``mass``\n\t\tSaves masses (field ``mass``) of spheres; active only if ``spheres`` is active.\n\t``clumpId``\n\t\tSaves id's of clumps to which each sphere belongs (field ``clumpId``); active only if ``spheres`` is active.\n\t``colors``\n\t\tSaves colors of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>` (field ``color``); only active if ``spheres`` or ``facets`` are activated.\n\t``mask``\n\t\tSaves groupMasks of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>` (field ``mask``); only active if ``spheres`` or ``facets`` are activated.\n\t``materialId``\n\t\tSaves materialID of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>`; only active if ``spheres`` or ``facets`` are activated.\n\t``velocity``\n\t\tSaves linear and angular velocities of spherical particles as Vector3 and length(fields ``linVelVec``, ``linVelLen`` and ``angVelVec``, ``angVelLen`` respectively``); only effective with ``spheres``.\n\t``stress``\n\t\tSaves stresses of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>` as Vector3 and length; only active if ``spheres`` or ``facets`` are activated.\n\t``pericell``\n\t\tSaves the shape of the cell (simulation has to be periodic).\n\t``bstresses``\n\t\tSaves per-particle principal stresses (sigI >= sigII >= sigIII) and associated principal directions (dirI/II/III). Per-particle stress tensors are given by :yref:`bodyStressTensors<yade.utils.bodyStressTensors>` (positive values for tensile states).\n\n.. admonition:: Specific recorders\n\n\tThe following should only be activated in appropriate cases, otherwise crashes can occur due to violation of type presuppositions.\n\n\t``cpm``\n\t\tSaves data pertaining to the :yref:`concrete model<Law2_ScGeom_CpmPhys_Cpm>`: ``cpmDamage`` (normalized residual strength averaged on particle), ``cpmStress`` (stress on particle); ``intr`` is activated automatically by ``cpm``\n\t``wpm``\n\t\tSaves data pertaining to the :yref:`wire particle model<Law2_ScGeom_WirePhys_WirePM>`: ``wpmForceNFactor`` shows the loading factor for the wire, e.g. normal force divided by threshold normal force.\n\t``jcfpm``\n\t\tSaves data pertaining to the :yref:`rock (smooth)-jointed model<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM>`: ``damage`` is defined by :yref:`JCFpmState.tensBreak` + :yref:`JCFpmState.shearBreak`; ``intr`` is activated automatically by ``jcfpm``, and :yref:`on joint<JCFpmPhys.isOnJoint>` or :yref:`cohesive<JCFpmPhys.isCohesive>` interactions can be vizualized.\n\t``cracks``\n\t\tSaves other data pertaining to the :yref:`rock model<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM>`: ``cracks`` shows locations where cohesive bonds failed during the simulation, with their types (0/1 for tensile/shear breakages), their sizes (0.5*(R1+R2)), and their normal directions. The :yref:`corresponding attribute<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.recordCracks>` has to be activated, and Key attributes have to be consistent.\n\n"))
+ ((vector<string>,recorders,vector<string>(1,string("all")),,"List of active recorders (as strings). ``all`` (the default value) enables all base and generic recorders.\n\n.. admonition:: Base recorders\n\n\tBase recorders save the geometry (unstructured grids) on which other data is defined. They are implicitly activated by many of the other recorders. Each of them creates a new file (or a block, if :yref:`multiblock <VTKRecorder.multiblock>` is set).\n\n\t``spheres``\n\t\tSaves positions and radii (``radii``) of :yref:`spherical<Sphere>` particles.\n\t``facets``\n\t\tSave :yref:`facets<Facet>` positions (vertices).\n\t``boxes``\n\t\tSave :yref:`boxes<Box>` positions (edges).\n\t``intr``\n\t\tStore interactions as lines between nodes at respective particles positions. Additionally stores magnitude of normal (``forceN``) and shear (``absForceT``) forces on interactions (the :yref:`geom<Interaction.geom> must be of type :yref:`NormShearPhys`). \n\n.. admonition:: Generic recorders\n\n\tGeneric recorders do not depend on specific model being used and save commonly useful data.\n\n\t``id``\n\t\tSaves id's (field ``id``) of spheres; active only if ``spheres`` is active.\n\t``mass``\n\t\tSaves masses (field ``mass``) of spheres; active only if ``spheres`` is active.\n\t``clumpId``\n\t\tSaves id's of clumps to which each sphere belongs (field ``clumpId``); active only if ``spheres`` is active.\n\t``colors``\n\t\tSaves colors of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>` (field ``color``); only active if ``spheres`` or ``facets`` are activated.\n\t``mask``\n\t\tSaves groupMasks of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>` (field ``mask``); only active if ``spheres`` or ``facets`` are activated.\n\t``materialId``\n\t\tSaves materialID of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>`; only active if ``spheres`` or ``facets`` are activated.\n\t``velocity``\n\t\tSaves linear and angular velocities of spherical particles as Vector3 and length(fields ``linVelVec``, ``linVelLen`` and ``angVelVec``, ``angVelLen`` respectively``); only effective with ``spheres``.\n\t``stress``\n\t\tSaves stresses of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>` as Vector3 and length; only active if ``spheres`` or ``facets`` are activated.\n\t``force``\n\t\tSaves force and torque of :yref:`spheres<Sphere>`, :yref:`facets<Facet>` and :yref:`boxes<Box>` as Vector3 and length (norm); only active if ``spheres``, ``facets`` or ``boxes`` are activated.\n\t``pericell``\n\t\tSaves the shape of the cell (simulation has to be periodic).\n\t``bstresses``\n\t\tSaves per-particle principal stresses (sigI >= sigII >= sigIII) and associated principal directions (dirI/II/III). Per-particle stress tensors are given by :yref:`bodyStressTensors<yade.utils.bodyStressTensors>` (positive values for tensile states).\n\n.. admonition:: Specific recorders\n\n\tThe following should only be activated in appropriate cases, otherwise crashes can occur due to violation of type presuppositions.\n\n\t``cpm``\n\t\tSaves data pertaining to the :yref:`concrete model<Law2_ScGeom_CpmPhys_Cpm>`: ``cpmDamage`` (normalized residual strength averaged on particle), ``cpmStress`` (stress on particle); ``intr`` is activated automatically by ``cpm``\n\t``wpm``\n\t\tSaves data pertaining to the :yref:`wire particle model<Law2_ScGeom_WirePhys_WirePM>`: ``wpmForceNFactor`` shows the loading factor for the wire, e.g. normal force divided by threshold normal force.\n\t``jcfpm``\n\t\tSaves data pertaining to the :yref:`rock (smooth)-jointed model<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM>`: ``damage`` is defined by :yref:`JCFpmState.tensBreak` + :yref:`JCFpmState.shearBreak`; ``intr`` is activated automatically by ``jcfpm``, and :yref:`on joint<JCFpmPhys.isOnJoint>` or :yref:`cohesive<JCFpmPhys.isCohesive>` interactions can be vizualized.\n\t``cracks``\n\t\tSaves other data pertaining to the :yref:`rock model<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM>`: ``cracks`` shows locations where cohesive bonds failed during the simulation, with their types (0/1 for tensile/shear breakages), their sizes (0.5*(R1+R2)), and their normal directions. The :yref:`corresponding attribute<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.recordCracks>` has to be activated, and Key attributes have to be consistent.\n\n"))
((string,Key,"",,"Necessary if :yref:`recorders<VTKRecorder.recorders>` contains 'cracks'. A string specifying the name of file 'cracks___.txt' that is considered in this case (see :yref:`corresponding attribute<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.Key>`)."))
((int,mask,0,,"If mask defined, only bodies with corresponding groupMask will be exported. If 0, all bodies will be exported.")),
/*ctor*/
=== modified file 'pkg/dem/ViscoelasticPM.cpp'
--- pkg/dem/ViscoelasticPM.cpp 2014-07-18 18:18:50 +0000
+++ pkg/dem/ViscoelasticPM.cpp 2014-08-26 14:53:06 +0000
@@ -170,7 +170,8 @@
mass2 = mass1;
}
- const Real massR = 2*mass1*mass2/(mass1+mass2);
+ // See [Pournin2001, just below equation (19)]
+ const Real massR = mass1*mass2/(mass1+mass2);
GenericSpheresContact* sphCont=YADE_CAST<GenericSpheresContact*>(interaction->geom.get());
Real R1=sphCont->refR1>0?sphCont->refR1:sphCont->refR2;
@@ -187,12 +188,19 @@
const Real Tc = (tc) ? (*tc)(mat1->id,mat2->id) : (mat1->tc+mat2->tc)/2.0;
const Real En = (en) ? (*en)(mat1->id,mat2->id) : (mat1->en+mat2->en)/2.0;
const Real Et = (et) ? (*et)(mat1->id,mat2->id) : (mat1->et+mat2->et)/2.0;
-
- kn1 = kn2 = 1/Tc/Tc * ( Mathr::PI*Mathr::PI + pow(log(En),2) )*massR;
- cn1 = cn2 = -2.0 /Tc * log(En)*massR;
- ks1 = ks2 = 2.0/7.0 /Tc/Tc * ( Mathr::PI*Mathr::PI + pow(log(Et),2) )*massR;
- cs1 = cs2 = -2.0/7.0 /Tc * log(Et)*massR;
-
+
+ // Factor 2 at the end of each expression is necessary, because we calculate
+ // individual kn1, kn2, ks1, ks2 etc., because kn1 = 2*kn, ks1 = 2*ks
+ // http://www.mail-archive.com/yade-users@xxxxxxxxxxxxxxxxxxx/msg08778.html
+ kn1 = kn2 = 1/Tc/Tc * ( Mathr::PI*Mathr::PI + pow(log(En),2) )*massR*2;
+ cn1 = cn2 = -2.0 /Tc * log(En)*massR*2;
+ ks1 = ks2 = 2.0/7.0 /Tc/Tc * ( Mathr::PI*Mathr::PI + pow(log(Et),2) )*massR*2;
+ cs1 = cs2 = -4.0/7.0 /Tc * log(Et)*massR*2;
+ // ^^^
+ // It seems to be an error in [Pournin2001] (22) Eq.4, missing factor 2
+ // Thanks to Dominik Boemer for pointing this out
+ // http://www.mail-archive.com/yade-users@xxxxxxxxxxxxxxxxxxx/msg08741.html
+
if (std::abs(cn1) <= Mathr::ZERO_TOLERANCE ) cn1=0;
if (std::abs(cn2) <= Mathr::ZERO_TOLERANCE ) cn2=0;
if (std::abs(cs1) <= Mathr::ZERO_TOLERANCE ) cs1=0;
=== modified file 'pkg/pfv/FlowEngine.hpp.in'
--- pkg/pfv/FlowEngine.hpp.in 2014-08-01 11:16:21 +0000
+++ pkg/pfv/FlowEngine.hpp.in 2014-09-03 15:59:54 +0000
@@ -225,7 +225,7 @@
((double, sineMagnitude, 0,, "Pressure value (amplitude) when sinusoidal pressure is applied (p )"))
((double, sineAverage, 0,,"Pressure value (average) when sinusoidal pressure is applied"))
((bool, debug, false,,"Activate debug messages"))
- ((double, wallThickness,0.001,,"Walls thickness"))
+ ((double, wallThickness,0,,"Walls thickness"))
((double,pZero,0,,"The value used for initializing pore pressure. It is useless for incompressible fluid, but important for compressible model."))
((double,tolerance,1e-06,,"Gauss-Seidel tolerance"))
((double,relax,1.9,,"Gauss-Seidel relaxation"))
=== modified file 'py/3rd-party/README'
--- py/3rd-party/README 2011-01-29 22:47:18 +0000
+++ py/3rd-party/README 2014-08-04 16:38:31 +0000
@@ -19,7 +19,7 @@
license: Boost software license 1.0
note: only headers are copied here
-mtTkinter-0.3:
+mtTkinter-0.4:
homepage: http://tkinter.unpythonic.net/wiki/mtTkinter
- source: http://tkinter.unpythonic.net/attach//mtTkinter/attachments/mtTkinter-0.3.tar.gz
- license: unspecified
+ source: http://tkinter.unpythonic.net/wiki/mtTkinter?action=AttachFile&do=get&target=mtTkinter-0.4.tar.gz
+ license: gpl lgpl
=== removed directory 'py/3rd-party/mtTkinter-0.3'
=== removed file 'py/3rd-party/mtTkinter-0.3/mtTkinter.py'
--- py/3rd-party/mtTkinter-0.3/mtTkinter.py 2010-07-06 11:31:29 +0000
+++ py/3rd-party/mtTkinter-0.3/mtTkinter.py 1970-01-01 00:00:00 +0000
@@ -1,227 +0,0 @@
-'''Thread-safe version of Tkinter.
-
-Usage:
-
- import mtTkinter as Tkinter
- # Use "Tkinter." as usual.
-
-or
-
- from mtTkinter import *
- # Use Tkinter module definitions as usual.
-
-This module modifies the original Tkinter module in memory, making all
-functionality thread-safe. It does this by wrapping the Tk class' tk
-instance with an object that diverts calls through an event queue when
-the call is issued from a thread other than the thread in which the Tk
-instance was created. The events are processed in the creation thread
-via an 'after' event.
-
-The modified Tk class accepts two additional keyword parameters on its
-__init__ method:
- mtDebug:
- 0 = No debug output (default)
- 1 = Minimal debug output
- ...
- 9 = Full debug output
- mtCheckPeriod:
- Amount of time in milliseconds (default 100) between checks for
- out-of-thread events when things are otherwise idle. Decreasing
- this value can improve GUI responsiveness, but at the expense of
- consuming more CPU cycles.
-
-Note that, because it modifies the original Tkinter module (in memory),
-other modules that use Tkinter (e.g., Pmw) reap the benefits automagically
-as long as mtTkinter is imported at some point before extra threads are
-created.
-
-Author: Allen B. Taylor, a.b.taylor@xxxxxxxxx
-'''
-
-from Tkinter import *
-import threading
-import Queue
-
-class _Tk(object):
- """
- Wrapper for underlying attribute tk of class Tk.
- """
-
- def __init__(self, tk, mtDebug = 0, mtCheckPeriod = 10):
- self._tk = tk
-
- # Create the incoming event queue.
- self._eventQueue = Queue.Queue(1)
-
- # Identify the thread from which this object is being created so we can
- # tell later whether an event is coming from another thread.
- self._creationThread = threading.currentThread()
-
- # Store remaining values.
- self._debug = mtDebug
- self._checkPeriod = mtCheckPeriod
-
- def __getattr__(self, name):
- # Divert attribute accesses to a wrapper around the underlying tk
- # object.
- return _TkAttr(self, getattr(self._tk, name))
-
-class _TkAttr(object):
- """
- Thread-safe callable attribute wrapper.
- """
-
- def __init__(self, tk, attr):
- self._tk = tk
- self._attr = attr
-
- def __call__(self, *args, **kwargs):
- """
- Thread-safe method invocation.
- Diverts out-of-thread calls through the event queue.
- Forwards all other method calls to the underlying tk object directly.
- """
-
- # Check if we're in the creation thread.
- if threading.currentThread() == self._tk._creationThread:
- # We're in the creation thread; just call the event directly.
- if self._tk._debug >= 8 or \
- self._tk._debug >= 3 and self._attr.__name__ == 'call' and \
- len(args) >= 1 and args[0] == 'after':
- print 'Calling event directly:', \
- self._attr.__name__, args, kwargs
- return self._attr(*args, **kwargs)
- else:
- # We're in a different thread than the creation thread; enqueue
- # the event, and then wait for the response.
- responseQueue = Queue.Queue(1)
- if self._tk._debug >= 1:
- print 'Marshalling event:', self._attr.__name__, args, kwargs
- self._tk._eventQueue.put((self._attr, args, kwargs, responseQueue))
- isException, response = responseQueue.get()
-
- # Handle the response, whether it's a normal return value or
- # an exception.
- if isException:
- exType, exValue, exTb = response
- raise exType, exValue, exTb
- else:
- return response
-
-# Define a hook for class Tk's __init__ method.
-def _Tk__init__(self, *args, **kwargs):
- # We support some new keyword arguments that the original __init__ method
- # doesn't expect, so separate those out before doing anything else.
- new_kwnames = ('mtCheckPeriod', 'mtDebug')
- new_kwargs = {}
- for name, value in kwargs.items():
- if name in new_kwnames:
- new_kwargs[name] = value
- del kwargs[name]
-
- # Call the original __init__ method, creating the internal tk member.
- self.__original__init__mtTkinter(*args, **kwargs)
-
- # Replace the internal tk member with a wrapper that handles calls from
- # other threads.
- self.tk = _Tk(self.tk, **new_kwargs)
-
- # Set up the first event to check for out-of-thread events.
- self.after_idle(_CheckEvents, self)
-
-# Replace Tk's original __init__ with the hook.
-Tk.__original__init__mtTkinter = Tk.__init__
-Tk.__init__ = _Tk__init__
-
-def _CheckEvents(tk):
- "Event checker event."
-
- used = False
- try:
- # Process all enqueued events, then exit.
- while True:
- try:
- # Get an event request from the queue.
- method, args, kwargs, responseQueue = \
- tk.tk._eventQueue.get_nowait()
- except:
- # No more events to process.
- break
- else:
- # Call the event with the given arguments, and then return
- # the result back to the caller via the response queue.
- used = True
- if tk.tk._debug >= 2:
- print 'Calling event from main thread:', \
- method.__name__, args, kwargs
- try:
- responseQueue.put((False, method(*args, **kwargs)))
- except SystemExit, ex:
- raise SystemExit, ex
- except Exception, ex:
- # Calling the event caused an exception; return the
- # exception back to the caller so that it can be raised
- # in the caller's thread.
- from sys import exc_info
- exType, exValue, exTb = exc_info()
- responseQueue.put((True, (exType, exValue, exTb)))
- finally:
- # Schedule to check again. If we just processed an event, check
- # immediately; if we didn't, check later.
- if used:
- tk.after_idle(_CheckEvents, tk)
- else:
- tk.after(tk.tk._checkPeriod, _CheckEvents, tk)
-
-# Test thread entry point.
-def _testThread(root):
- text = "This is Tcl/Tk version %s" % TclVersion
- if TclVersion >= 8.1:
- try:
- text = text + unicode("\nThis should be a cedilla: \347",
- "iso-8859-1")
- except NameError:
- pass # no unicode support
- try:
- if root.globalgetvar('tcl_platform(threaded)'):
- text = text + "\nTcl is built with thread support"
- else:
- raise RuntimeError
- except:
- text = text + "\nTcl is NOT built with thread support"
- text = text + "\nmtTkinter works with or without Tcl thread support"
- label = Label(root, text=text)
- label.pack()
- button = Button(root, text="Click me!",
- command=lambda root=root: root.button.configure(
- text="[%s]" % root.button['text']))
- button.pack()
- root.button = button
- quit = Button(root, text="QUIT", command=root.destroy)
- quit.pack()
- # The following three commands are needed so the window pops
- # up on top on Windows...
- root.iconify()
- root.update()
- root.deiconify()
- # Simulate button presses...
- button.invoke()
- root.after(1000, _pressOk, root, button)
-
-# Test button continuous press event.
-def _pressOk(root, button):
- button.invoke()
- try:
- root.after(1000, _pressOk, root, button)
- except:
- pass # Likely we're exiting
-
-# Test. Mostly borrowed from the Tkinter module, but the important bits moved
-# into a separate thread.
-if __name__ == '__main__':
- import threading
- root = Tk(mtDebug = 1)
- thread = threading.Thread(target = _testThread, args=(root,))
- thread.start()
- root.mainloop()
- thread.join()
=== added directory 'py/3rd-party/mtTkinter-0.4'
=== added file 'py/3rd-party/mtTkinter-0.4/gpl.txt'
--- py/3rd-party/mtTkinter-0.4/gpl.txt 1970-01-01 00:00:00 +0000
+++ py/3rd-party/mtTkinter-0.4/gpl.txt 2014-08-04 16:38:31 +0000
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+ The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users. We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors. You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+ To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights. Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received. You must make sure that they, too, receive
+or can get the source code. And you must show them these terms so they
+know their rights.
+
+ Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+ For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software. For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+ Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so. This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software. The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable. Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products. If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+ Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary. To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ TERMS AND CONDITIONS
+
+ 0. Definitions.
+
+ "This License" refers to version 3 of the GNU General Public License.
+
+ "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+ "The Program" refers to any copyrightable work licensed under this
+License. Each licensee is addressed as "you". "Licensees" and
+"recipients" may be individuals or organizations.
+
+ To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy. The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+ A "covered work" means either the unmodified Program or a work based
+on the Program.
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+ If you develop a new program, and you want it to be of the greatest
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+ This is free software, and you are welcome to redistribute it
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+The hypothetical commands `show w' and `show c' should show the appropriate
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+if any, to sign a "copyright disclaimer" for the program, if necessary.
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+may consider it more useful to permit linking proprietary applications with
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+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
=== added file 'py/3rd-party/mtTkinter-0.4/lgpl.txt'
--- py/3rd-party/mtTkinter-0.4/lgpl.txt 1970-01-01 00:00:00 +0000
+++ py/3rd-party/mtTkinter-0.4/lgpl.txt 2014-08-04 16:38:31 +0000
@@ -0,0 +1,165 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+ This version of the GNU Lesser General Public License incorporates
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+License, supplemented by the additional permissions listed below.
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+Library.
=== added file 'py/3rd-party/mtTkinter-0.4/mtTkinter.py'
--- py/3rd-party/mtTkinter-0.4/mtTkinter.py 1970-01-01 00:00:00 +0000
+++ py/3rd-party/mtTkinter-0.4/mtTkinter.py 2014-08-04 16:38:31 +0000
@@ -0,0 +1,242 @@
+'''Thread-safe version of Tkinter.
+
+Copyright (c) 2009, Allen B. Taylor
+
+This module is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU Lesser Public License for more details.
+
+You should have received a copy of the GNU Lesser Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Usage:
+
+ import mtTkinter as Tkinter
+ # Use "Tkinter." as usual.
+
+or
+
+ from mtTkinter import *
+ # Use Tkinter module definitions as usual.
+
+This module modifies the original Tkinter module in memory, making all
+functionality thread-safe. It does this by wrapping the Tk class' tk
+instance with an object that diverts calls through an event queue when
+the call is issued from a thread other than the thread in which the Tk
+instance was created. The events are processed in the creation thread
+via an 'after' event.
+
+The modified Tk class accepts two additional keyword parameters on its
+__init__ method:
+ mtDebug:
+ 0 = No debug output (default)
+ 1 = Minimal debug output
+ ...
+ 9 = Full debug output
+ mtCheckPeriod:
+ Amount of time in milliseconds (default 100) between checks for
+ out-of-thread events when things are otherwise idle. Decreasing
+ this value can improve GUI responsiveness, but at the expense of
+ consuming more CPU cycles.
+
+Note that, because it modifies the original Tkinter module (in memory),
+other modules that use Tkinter (e.g., Pmw) reap the benefits automagically
+as long as mtTkinter is imported at some point before extra threads are
+created.
+
+Author: Allen B. Taylor, a.b.taylor@xxxxxxxxx
+'''
+
+from Tkinter import *
+import threading
+import Queue
+
+class _Tk(object):
+ """
+ Wrapper for underlying attribute tk of class Tk.
+ """
+
+ def __init__(self, tk, mtDebug = 0, mtCheckPeriod = 10):
+ self._tk = tk
+
+ # Create the incoming event queue.
+ self._eventQueue = Queue.Queue(1)
+
+ # Identify the thread from which this object is being created so we can
+ # tell later whether an event is coming from another thread.
+ self._creationThread = threading.currentThread()
+
+ # Store remaining values.
+ self._debug = mtDebug
+ self._checkPeriod = mtCheckPeriod
+
+ def __getattr__(self, name):
+ # Divert attribute accesses to a wrapper around the underlying tk
+ # object.
+ return _TkAttr(self, getattr(self._tk, name))
+
+class _TkAttr(object):
+ """
+ Thread-safe callable attribute wrapper.
+ """
+
+ def __init__(self, tk, attr):
+ self._tk = tk
+ self._attr = attr
+
+ def __call__(self, *args, **kwargs):
+ """
+ Thread-safe method invocation.
+ Diverts out-of-thread calls through the event queue.
+ Forwards all other method calls to the underlying tk object directly.
+ """
+
+ # Check if we're in the creation thread.
+ if threading.currentThread() == self._tk._creationThread:
+ # We're in the creation thread; just call the event directly.
+ if self._tk._debug >= 8 or \
+ self._tk._debug >= 3 and self._attr.__name__ == 'call' and \
+ len(args) >= 1 and args[0] == 'after':
+ print 'Calling event directly:', \
+ self._attr.__name__, args, kwargs
+ return self._attr(*args, **kwargs)
+ else:
+ # We're in a different thread than the creation thread; enqueue
+ # the event, and then wait for the response.
+ responseQueue = Queue.Queue(1)
+ if self._tk._debug >= 1:
+ print 'Marshalling event:', self._attr.__name__, args, kwargs
+ self._tk._eventQueue.put((self._attr, args, kwargs, responseQueue))
+ isException, response = responseQueue.get()
+
+ # Handle the response, whether it's a normal return value or
+ # an exception.
+ if isException:
+ exType, exValue, exTb = response
+ raise exType, exValue, exTb
+ else:
+ return response
+
+# Define a hook for class Tk's __init__ method.
+def _Tk__init__(self, *args, **kwargs):
+ # We support some new keyword arguments that the original __init__ method
+ # doesn't expect, so separate those out before doing anything else.
+ new_kwnames = ('mtCheckPeriod', 'mtDebug')
+ new_kwargs = {}
+ for name, value in kwargs.items():
+ if name in new_kwnames:
+ new_kwargs[name] = value
+ del kwargs[name]
+
+ # Call the original __init__ method, creating the internal tk member.
+ self.__original__init__mtTkinter(*args, **kwargs)
+
+ # Replace the internal tk member with a wrapper that handles calls from
+ # other threads.
+ self.tk = _Tk(self.tk, **new_kwargs)
+
+ # Set up the first event to check for out-of-thread events.
+ self.after_idle(_CheckEvents, self)
+
+# Replace Tk's original __init__ with the hook.
+Tk.__original__init__mtTkinter = Tk.__init__
+Tk.__init__ = _Tk__init__
+
+def _CheckEvents(tk):
+ "Event checker event."
+
+ used = False
+ try:
+ # Process all enqueued events, then exit.
+ while True:
+ try:
+ # Get an event request from the queue.
+ method, args, kwargs, responseQueue = \
+ tk.tk._eventQueue.get_nowait()
+ except:
+ # No more events to process.
+ break
+ else:
+ # Call the event with the given arguments, and then return
+ # the result back to the caller via the response queue.
+ used = True
+ if tk.tk._debug >= 2:
+ print 'Calling event from main thread:', \
+ method.__name__, args, kwargs
+ try:
+ responseQueue.put((False, method(*args, **kwargs)))
+ except SystemExit, ex:
+ raise SystemExit, ex
+ except Exception, ex:
+ # Calling the event caused an exception; return the
+ # exception back to the caller so that it can be raised
+ # in the caller's thread.
+ from sys import exc_info
+ exType, exValue, exTb = exc_info()
+ responseQueue.put((True, (exType, exValue, exTb)))
+ finally:
+ # Schedule to check again. If we just processed an event, check
+ # immediately; if we didn't, check later.
+ if used:
+ tk.after_idle(_CheckEvents, tk)
+ else:
+ tk.after(tk.tk._checkPeriod, _CheckEvents, tk)
+
+# Test thread entry point.
+def _testThread(root):
+ text = "This is Tcl/Tk version %s" % TclVersion
+ if TclVersion >= 8.1:
+ try:
+ text = text + unicode("\nThis should be a cedilla: \347",
+ "iso-8859-1")
+ except NameError:
+ pass # no unicode support
+ try:
+ if root.globalgetvar('tcl_platform(threaded)'):
+ text = text + "\nTcl is built with thread support"
+ else:
+ raise RuntimeError
+ except:
+ text = text + "\nTcl is NOT built with thread support"
+ text = text + "\nmtTkinter works with or without Tcl thread support"
+ label = Label(root, text=text)
+ label.pack()
+ button = Button(root, text="Click me!",
+ command=lambda root=root: root.button.configure(
+ text="[%s]" % root.button['text']))
+ button.pack()
+ root.button = button
+ quit = Button(root, text="QUIT", command=root.destroy)
+ quit.pack()
+ # The following three commands are needed so the window pops
+ # up on top on Windows...
+ root.iconify()
+ root.update()
+ root.deiconify()
+ # Simulate button presses...
+ button.invoke()
+ root.after(1000, _pressOk, root, button)
+
+# Test button continuous press event.
+def _pressOk(root, button):
+ button.invoke()
+ try:
+ root.after(1000, _pressOk, root, button)
+ except:
+ pass # Likely we're exiting
+
+# Test. Mostly borrowed from the Tkinter module, but the important bits moved
+# into a separate thread.
+if __name__ == '__main__':
+ import threading
+ root = Tk(mtDebug = 1)
+ thread = threading.Thread(target = _testThread, args=(root,))
+ thread.start()
+ root.mainloop()
+ thread.join()
=== modified file 'py/CMakeLists.txt'
--- py/CMakeLists.txt 2013-10-15 16:14:46 +0000
+++ py/CMakeLists.txt 2014-08-04 16:38:31 +0000
@@ -21,7 +21,7 @@
FILE(GLOB filesPY "${CMAKE_CURRENT_SOURCE_DIR}/*.py")
SET(filesPY "${filesPY};${CMAKE_CURRENT_SOURCE_DIR}/pack/pack.py")
INSTALL(FILES ${filesPY} DESTINATION ${YADE_PY_PATH}/yade)
-INSTALL(FILES 3rd-party/mtTkinter-0.3/mtTkinter.py DESTINATION ${YADE_LIB_PATH}/py)
+INSTALL(FILES 3rd-party/mtTkinter-0.4/mtTkinter.py DESTINATION ${YADE_LIB_PATH}/py)
FILE(GLOB filesPYTests "${CMAKE_CURRENT_SOURCE_DIR}/tests/*.py")
INSTALL(FILES ${filesPYTests} DESTINATION ${YADE_PY_PATH}/yade/tests)
FILE(GLOB filesPYPerf "${CMAKE_CURRENT_SOURCE_DIR}/../examples/test/performance/*")
=== modified file 'py/_utils.cpp'
--- py/_utils.cpp 2014-08-01 17:25:38 +0000
+++ py/_utils.cpp 2014-09-03 17:34:07 +0000
@@ -488,7 +488,7 @@
py::def("fabricTensor",Shop__fabricTensor,(py::args("splitTensor")=false,py::args("revertSign")=false,py::args("thresholdForce")=NaN),"Compute the fabric tensor of the periodic cell. The original paper can be found in [Satake1982]_.\n\n:param bool splitTensor: split the fabric tensor into two parts related to the strong and weak contact forces respectively.\n\n:param bool revertSign: it must be set to true if the contact law's convention takes compressive forces as positive.\n\n:param Real thresholdForce: if the fabric tensor is split into two parts, a threshold value can be specified otherwise the mean contact force is considered by default. It is worth to note that this value has a sign and the user needs to set it according to the convention adopted for the contact law. To note that this value could be set to zero if one wanted to make distinction between compressive and tensile forces.");
py::def("bodyStressTensors",Shop__getStressLWForEachBody,"Compute and return a table with per-particle stress tensors. Each tensor represents the average stress in one particle, obtained from the contour integral of applied load as detailed below. This definition is considering each sphere as a continuum. It can be considered exact in the context of spheres at static equilibrium, interacting at contact points with negligible volume changes of the solid phase (this last assumption is not restricting possible deformations and volume changes at the packing scale).\n\nProof: \n\nFirst, we remark the identity: $\\sigma_{ij}=\\delta_{ik}\\sigma_{kj}=x_{i,k}\\sigma_{kj}=(x_{i}\\sigma_{kj})_{,k}-x_{i}\\sigma_{kj,k}$.\n\nAt equilibrium, the divergence of stress is null: $\\sigma_{kj,k}=\\vec{0}$. Consequently, after divergence theorem: $\\frac{1}{V}\\int_V \\sigma_{ij}dV = \\frac{1}{V}\\int_V (x_{i}\\sigma_{kj})_{,k}dV = \\frac{1}{V}\\int_{\\partial V}x_i\\sigma_{kj}n_kdS = \\frac{1}{V}\\sum_bx_i^bf_j^b$.\n\nThe last equality is implicitely based on the representation of external loads as Dirac distributions whose zeros are the so-called *contact points*: 0-sized surfaces on which the *contact forces* are applied, located at $x_i$ in the deformed configuration.\n\nA weighted average of per-body stresses will give the average stress inside the solid phase. There is a simple relation between the stress inside the solid phase and the stress in an equivalent continuum in the absence of fluid pressure. For porosity $n$, the relation reads: $\\sigma_{ij}^{equ.}=(1-n)\\sigma_{ij}^{solid}$.\n\nThis last relation may not be very useful if porosity is not homogeneous. If it happens, one can define the equivalent bulk stress a the particles scale by assigning a volume to each particle. This volume can be obtained from :yref:`TesselationWrapper` (see e.g. [Catalano2014a]_)");
py::def("getStress",Shop::getStress,(py::args("volume")=0),"Compute and return Love-Weber stress tensor:\n\n $\\sigma_{ij}=\\frac{1}{V}\\sum_b f_i^b l_j^b$, where the sum is over all interactions, with $f$ the contact force and $l$ the branch vector (joining centers of the bodies). Stress is negativ for repulsive contact forces, i.e. compression. $V$ can be passed to the function. If it is not, it will be equal to one in non-periodic cases, or equal to the volume of the cell in periodic cases.");
- py::def("getCapillaryStress",Shop::getCapillaryStress,(py::args("volume")=0),"Compute and return Love-Weber capillary stress tensor:\n\n $\\sigma^{cap}_{ij}=\\frac{1}{V}\\sum_b l_i^b f^{cap,b}_j$, where the sum is over all interactions, with $l$ the branch vector (joining centers of the bodies) and $f^{cap}$ is the capillary force. $V$ can be passed to the function. If it is not, it will be equal to one in non-periodic cases, or equal to the volume of the cell in periodic cases. Only the CapillaryPhys interaction type is supported presently.");
+ py::def("getCapillaryStress",Shop::getCapillaryStress,(py::args("volume")=0,py::args("mindlin")=false),"Compute and return Love-Weber capillary stress tensor:\n\n $\\sigma^{cap}_{ij}=\\frac{1}{V}\\sum_b l_i^b f^{cap,b}_j$, where the sum is over all interactions, with $l$ the branch vector (joining centers of the bodies) and $f^{cap}$ is the capillary force. $V$ can be passed to the function. If it is not, it will be equal to one in non-periodic cases, or equal to the volume of the cell in periodic cases. Only the CapillaryPhys interaction type is supported presently. Using this function with physics MindlinCapillaryPhys needs to pass True as second argument.");
py::def("getBodyIdsContacts",Shop__getBodyIdsContacts,(py::args("bodyID")=0),"Get a list of body-ids, which contacts the given body.");
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.");
py::def("shiftBodies",shiftBodies,(py::arg("ids"),py::arg("shift")),"Shifts bodies listed in ids without updating their velocities.");
=== modified file 'py/pack/_packSpheres.cpp'
--- py/pack/_packSpheres.cpp 2014-05-23 13:03:50 +0000
+++ py/pack/_packSpheres.cpp 2014-09-03 15:59:54 +0000
@@ -15,17 +15,19 @@
.def("load",&SpherePack::fromFile,(boost::python::arg("fileName")),"Load packing from external text file (current data will be discarded).")
.def("save",&SpherePack::toFile,(boost::python::arg("fileName")),"Save packing to external text file (will be overwritten).")
.def("fromSimulation",&SpherePack::fromSimulation,"Make packing corresponding to the current simulation. Discards current data.")
+ //The basic sphere generator
.def("makeCloud",&SpherePack::makeCloud,(boost::python::arg("minCorner")=Vector3r(Vector3r::Zero()),boost::python::arg("maxCorner")=Vector3r(Vector3r::Zero()),boost::python::arg("rMean")=-1,boost::python::arg("rRelFuzz")=0,boost::python::arg("num")=-1,boost::python::arg("periodic")=false,boost::python::arg("porosity")=0.65,boost::python::arg("psdSizes")=vector<Real>(),boost::python::arg("psdCumm")=vector<Real>(),boost::python::arg("distributeMass")=false,boost::python::arg("seed")=0,boost::python::arg("hSize")=Matrix3r(Matrix3r::Zero())),"Create random loose packing enclosed in a parallelepiped (also works in 2D if minCorner[k]=maxCorner[k] for one coordinate)."
"\nSphere radius distribution can be specified using one of the following ways:\n\n#. *rMean*, *rRelFuzz* and *num* gives uniform radius distribution in *rMean×(1 ± rRelFuzz)*. Less than *num* spheres can be generated if it is too high.\n#. *rRelFuzz*, *num* and (optional) *porosity*, which estimates mean radius so that *porosity* is attained at the end. *rMean* must be less than 0 (default). *porosity* is only an initial guess for the generation algorithm, which will retry with higher porosity until the prescibed *num* is obtained.\n#. *psdSizes* and *psdCumm*, two arrays specifying points of the `particle size distribution <http://en.wikipedia.org/wiki/Particle_size_distribution>`__ function. As many spheres as possible are generated.\n#. *psdSizes*, *psdCumm*, *num*, and (optional) *porosity*, like above but if *num* is not obtained, *psdSizes* will be scaled down uniformly, until *num* is obtained (see :yref:`appliedPsdScaling<yade._packSpheres.SpherePack.appliedPsdScaling>`).\n\nBy default (with ``distributeMass==False``), the distribution is applied to particle radii. The usual sense of \"particle size distribution\" is the distribution of *mass fraction* (rather than particle count); this can be achieved with ``distributeMass=True``."
"\n\nIf *num* is defined, then sizes generation is deterministic, giving the best fit of target distribution. It enables spheres placement in descending size order, thus giving lower porosity than the random generation."
"\n\n:param Vector3 minCorner: lower corner of an axis-aligned box\n:param Vector3 maxCorner: upper corner of an axis-aligned box\n:param Matrix3 hSize: base vectors of a generalized box (arbitrary parallelepiped, typically :yref:`Cell::hSize`), superseeds minCorner and maxCorner if defined. For periodic boundaries only.\n:param float rMean: mean radius or spheres\n:param float rRelFuzz: dispersion of radius relative to rMean\n:param int num: number of spheres to be generated. If negavite (default), generate as many as possible with stochastic sizes, ending after a fixed number of tries to place the sphere in space, else generate exactly *num* spheres with deterministic size distribution.\n:param bool periodic: whether the packing to be generated should be periodic\n:param float porosity: initial guess for the iterative generation procedure (if *num*>1). The algorithm will be retrying until the number of generated spheres is *num*. The first iteration tries with the provided porosity, but next iterations increase it if necessary (hence an initialy high porosity can speed-up the algorithm). If *psdSizes* is not defined, *rRelFuzz* ($z$) and *num* ($N$) are used so that the porosity given ($\\rho$) is approximately achieved at the end of generation, $r_m=\\sqrt[3]{\\frac{V(1-\\rho)}{\\frac{4}{3}\\pi(1+z^2)N}}$. The default is $\\rho$=0.5. The optimal value depends on *rRelFuzz* or *psdSizes*.\n:param psdSizes: sieve sizes (particle diameters) when particle size distribution (PSD) is specified\n:param psdCumm: cummulative fractions of particle sizes given by *psdSizes*; must be the same length as *psdSizes* and should be non-decreasing\n:param bool distributeMass: if ``True``, given distribution will be used to distribute sphere's mass rather than radius of them.\n:param seed: number used to initialize the random number generator.\n:returns: number of created spheres, which can be lower than *num* depending on the method used.\n")
.def("psd",&SpherePack::psd,(boost::python::arg("bins")=50,boost::python::arg("mass")=true),"Return `particle size distribution <http://en.wikipedia.org/wiki/Particle_size_distribution>`__ of the packing.\n:param int bins: number of bins between minimum and maximum diameter\n:param mass: Compute relative mass rather than relative particle count for each bin. Corresponds to :yref:`distributeMass parameter for makeCloud<yade.pack.SpherePack.makeCloud>`.\n:returns: tuple of ``(cumm,edges)``, where ``cumm`` are cummulative fractions for respective diameters and ``edges`` are those diameter values. Dimension of both arrays is equal to ``bins+1``.")
- // new psd
- .def("particleSD",&SpherePack::particleSD,(boost::python::arg("minCorner"),boost::python::arg("maxCorner"),boost::python::arg("rMean"),boost::python::arg("periodic")=false,boost::python::arg("name"),boost::python::arg("numSph"),boost::python::arg("radii")=vector<Real>(),boost::python::arg("passing")=vector<Real>(),boost::python::arg("passingIsNotPercentageButCount")=false, boost::python::arg("seed")=0),"Create random packing enclosed in box given by minCorner and maxCorner, containing numSph spheres. Returns number of created spheres, which can be < num if the packing is too tight. The computation is done according to the given psd.")
- .def("particleSD2",&SpherePack::particleSD2,(boost::python::arg("radii"),boost::python::arg("passing"),boost::python::arg("numSph"),boost::python::arg("periodic")=false,boost::python::arg("cloudPorosity")=.8,boost::python::arg("seed")=0),"Create random packing following the given particle size distribution (radii and volume/mass passing for each fraction) and total number of particles *numSph*. The cloud size (periodic or aperiodic) is computed from the PSD and is always cubic.")
- .def("particleSD_2d",&SpherePack::particleSD_2d,(boost::python::arg("minCorner"),boost::python::arg("maxCorner"),boost::python::arg("rMean"),boost::python::arg("periodic")=false,boost::python::arg("name"),boost::python::arg("numSph"),boost::python::arg("radii")=vector<Real>(),boost::python::arg("passing")=vector<Real>(),boost::python::arg("passingIsNotPercentageButCount")=false,boost::python::arg("seed")=0),"Create random packing on XY plane, defined by minCorner and maxCorner, containing numSph spheres. Returns number of created spheres, which can be < num if the packing is too tight. The computation is done according to the given psd.")
-
+ //The variant for clumps
.def("makeClumpCloud",&SpherePack::makeClumpCloud,(boost::python::arg("minCorner"),boost::python::arg("maxCorner"),boost::python::arg("clumps"),boost::python::arg("periodic")=false,boost::python::arg("num")=-1,boost::python::arg("seed")=0),"Create random loose packing of clumps within box given by *minCorner* and *maxCorner*. Clumps are selected with equal probability. At most *num* clumps will be positioned if *num* is positive; otherwise, as many clumps as possible will be put in space, until maximum number of attempts to place a new clump randomly is attained.\n:param seed: number used to initialize the random number generator.")
+ // old unmaintained stuff, kept for the moment so it at least returns an error message
+ .def("particleSD",&SpherePack::particleSD,(boost::python::arg("minCorner"),boost::python::arg("maxCorner"),boost::python::arg("rMean"),boost::python::arg("periodic")=false,boost::python::arg("name"),boost::python::arg("numSph"),boost::python::arg("radii")=vector<Real>(),boost::python::arg("passing")=vector<Real>(),boost::python::arg("passingIsNotPercentageButCount")=false, boost::python::arg("seed")=0),"Not working. Use makeCloud instead.")
+ .def("particleSD2",&SpherePack::particleSD2,(boost::python::arg("radii"),boost::python::arg("passing"),boost::python::arg("numSph"),boost::python::arg("periodic")=false,boost::python::arg("cloudPorosity")=.8,boost::python::arg("seed")=0),"Not working. Use makeCloud instead.")
+ .def("particleSD_2d",&SpherePack::particleSD_2d,(boost::python::arg("minCorner"),boost::python::arg("maxCorner"),boost::python::arg("rMean"),boost::python::arg("periodic")=false,boost::python::arg("name"),boost::python::arg("numSph"),boost::python::arg("radii")=vector<Real>(),boost::python::arg("passing")=vector<Real>(),boost::python::arg("passingIsNotPercentageButCount")=false,boost::python::arg("seed")=0),"Not working. Use makeCloud instead.")
+
//
.def("aabb",&SpherePack::aabb_py,"Get axis-aligned bounding box coordinates, as 2 3-tuples.")
.def("dim",&SpherePack::dim,"Return dimensions of the packing in terms of aabb(), as a 3-tuple.")
=== modified file 'py/utils.py'
--- py/utils.py 2014-07-22 17:23:17 +0000
+++ py/utils.py 2014-08-21 14:31:08 +0000
@@ -391,7 +391,7 @@
return b
def polyhedron(vertices,dynamic=True,fixed=False,wire=True,color=None,highlight=False,noBound=False,material=-1,mask=1,chain=-1):
- """Create tetrahedron (actually simple Polyhedra) with given parameters.
+ """Create polyhedron with given parameters.
:param [Vector3,Vector3,Vector3,Vector3] vertices: coordinates of vertices in the global coordinate system.
=== modified file 'scripts/checks-and-tests/checks/DEM-PFV-check.py'
--- scripts/checks-and-tests/checks/DEM-PFV-check.py 2014-07-28 06:50:17 +0000
+++ scripts/checks-and-tests/checks/DEM-PFV-check.py 2014-08-07 13:38:16 +0000
@@ -5,7 +5,8 @@
if ('PFVFLOW' in features):
errors=0
- tolerance=0.01
+ toleranceWarning =0.01
+ toleranceCritical=0.10
from yade import pack
num_spheres=100# number of spheres
@@ -77,9 +78,11 @@
modulus = 1000./abs(e22)
target=252759.905803
- if abs((modulus-target)/target)>tolerance :
+ if abs((modulus-target)/target)>toleranceWarning:
print "DEM-PFV: difference in bulk modulus:", modulus, "vs. target ",target
- errors+=1
+ if (abs((modulus-target)/target)>toleranceCritical):
+ errors+=1
+ print "The difference is more, than the critical tolerance!"
#B. Activate flow engine and set boundary conditions in order to get permeability
flow.dead=0
@@ -103,9 +106,11 @@
errors+=1
target=0.040399916554
- if abs((permeability-target)/target)>tolerance :
+ if abs((permeability-target)/target)>toleranceWarning:
print "DEM-PFV: difference in permeability:",permeability," vs. target ",target
- errors+=1
+ if (abs((permeability-target)/target)>toleranceCritical):
+ errors+=1
+ print "The difference is more, than the critical tolerance!"
#C. now the oedometer test, drained at the top, impermeable at the bottom plate
flow.bndCondIsPressure=[0,0,0,1,0,0]
@@ -121,13 +126,19 @@
O.run(3000,1)
target=628.314160434
- if abs((flow.getPorePressure((0.5,0.1,0.5))-target)/target)>tolerance :
+ if abs((flow.getPorePressure((0.5,0.1,0.5))-target)/target)>toleranceWarning:
print "DEM-PFV: difference in final pressure:",flow.getPorePressure((0.5,0.1,0.5))," vs. target ",target
- errors+=1
+ if (abs((flow.getPorePressure((0.5,0.1,0.5))-target)/target)>toleranceCritical):
+ errors+=1
+ print "The difference is more, than the critical tolerance!"
+
target=0.00258113045083
- if abs((triax.strain[1]-zeroe22-target)/target)>tolerance :
+ if abs((triax.strain[1]-zeroe22-target)/target)>toleranceWarning:
print "DEM-PFV: difference in final deformation",triax.strain[1]-zeroe22," vs. target ",target
- errors+=1
+ if (abs((triax.strain[1]-zeroe22-target)/target)>toleranceCritical):
+ errors+=1
+ print "The difference is more, than the critical tolerance!"
+
if (float(flow.execTime)/float(sum([e.execTime for e in O.engines])))>0.6 :
print "(INFO) DEM-PFV: More than 60\% of cpu time in FlowEngine (",100.*(float(flow.execTime)/float(sum([e.execTime for e in O.engines]))) ,"%). Should not happen with efficient libraries (check blas/lapack/cholmod implementations)"
=== added file 'scripts/checks-and-tests/checks/checkClumpHopper.py'
--- scripts/checks-and-tests/checks/checkClumpHopper.py 1970-01-01 00:00:00 +0000
+++ scripts/checks-and-tests/checks/checkClumpHopper.py 2014-08-18 22:44:44 +0000
@@ -0,0 +1,80 @@
+# -*- coding: utf-8
+# This script is used in --check to keep the functionality of adding/removal
+# of particles and clumps functional
+
+import itertools
+from numpy import *
+
+
+kinEnergyMax = 100000
+# Parameters
+tc=0.001# collision time
+en=.3 # normal restitution coefficient
+es=.3 # tangential restitution coefficient
+frictionAngle=radians(35)#
+density=2700
+# facets material
+facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es))
+# default spheres material
+dfltSpheresMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es))
+
+O.dt=.05*tc # time step
+
+Rs=0.05 # particle radius
+
+# Create geometry
+
+x0=0.; y0=0.; z0=0.; ab=.7; at=2.; h=1.; hl=h; al=at*3
+
+zb=z0; x0b=x0-ab/2.; y0b=y0-ab/2.; x1b=x0+ab/2.; y1b=y0+ab/2.
+zt=z0+h; x0t=x0-at/2.; y0t=y0-at/2.; x1t=x0+at/2.; y1t=y0+at/2.
+zl=z0-hl;x0l=x0-al/2.; y0l=y0-al/2.; x1l=x0+al/2.; y1l=y0+al/2.
+
+vibrationPlate = O.bodies.append(geom.facetBunker((x0,y0,z0),
+ dBunker=ab*4.0,dOutput=ab*1.7,hBunker=ab*3,hOutput=ab,hPipe=ab/3.0,
+ wallMask=4,segmentsNumber=10,material=facetMat))
+
+# Create engines
+O.engines=[
+ ForceResetter(),
+ InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),
+ InteractionLoop(
+ [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()],
+ [Ip2_ViscElMat_ViscElMat_ViscElPhys()],
+ [Law2_ScGeom_ViscElPhys_Basic()],
+ ),
+ DomainLimiter(lo=(-4,-4,-1),hi=(4,4,4),iterPeriod=5000,label='domLim'),
+ NewtonIntegrator(damping=0, gravity=[0,0,-9.81]),
+ PyRunner(iterPeriod=6500,command='addBodies()',nDo=7,label='addb'),
+ PyRunner(iterPeriod=10000,command='state()',label='state'),
+]
+
+numSphereGen = 0
+def addBodies():
+ global numSphereGen
+ # Create clumps...
+ clumpColor=(0.0, 0.5, 0.5)
+ for k,l in itertools.product(arange(0,10),arange(0,10)):
+ clpId,sphId=O.bodies.appendClumped([sphere(Vector3(x0t+Rs*(k*4+2),y0t+Rs*(l*4+2),i*Rs*2+zt+ab*3),Rs,color=clumpColor,material=dfltSpheresMat) for i in xrange(4)])
+ numSphereGen += len(sphId)
+
+ # ... and spheres
+ spheresColor=(0.4, 0.4, 0.4)
+ for k,l in itertools.product(arange(0,9),arange(0,9)):
+ sphAloneId=O.bodies.append( [sphere( Vector3(x0t+Rs*(k*4+4),y0t+Rs*(l*4+4),i*Rs*2.3+zt+ab*3),Rs,color=spheresColor,material=dfltSpheresMat) for i in xrange(4) ] )
+ numSphereGen += len(sphAloneId)
+
+def state():
+ global numSphereGen
+ global resultStatus
+ print "Iter %d: Total number of generated spheres %d, removed particles %d, current particles %d, kinEnergy %g"%(O.iter, numSphereGen, domLim.nDeleted, numSphereGen-domLim.nDeleted, utils.kineticEnergy())
+ if (utils.kineticEnergy() > kinEnergyMax):
+ print "Kinetic energy is over a threshold value! Error!"
+ resultStatus += 1
+ O.pause()
+
+addBodies()
+O.run(10, True)
+O.bodies.erase(64, True)
+
+O.run(50002, True)
=== modified file 'scripts/checks-and-tests/checks/checkViscElEng.py'
--- scripts/checks-and-tests/checks/checkViscElEng.py 2014-04-02 15:33:41 +0000
+++ scripts/checks-and-tests/checks/checkViscElEng.py 2014-08-26 14:53:06 +0000
@@ -45,8 +45,8 @@
if v0<=0 and v>0:
en=-v/v0
- print ("Precalculated en value %f" % 0.736356797441)
- print ("Obtained en value %f" % en)
+ print ("Precalculated en value %.12f" % 0.736356797441)
+ print ("Obtained en value %.12f" % en)
O.pause()
v0=v
=== added file 'scripts/checks-and-tests/checks/checkViscElPM.py'
--- scripts/checks-and-tests/checks/checkViscElPM.py 1970-01-01 00:00:00 +0000
+++ scripts/checks-and-tests/checks/checkViscElPM.py 2014-08-27 18:41:41 +0000
@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+################################################################################
+# CONSTITUTIVE LAW TESTING: Law2_ScGeom_ViscElPhys_Basic()
+#
+# Two spheres with velocities (v,0,0) and (-v,0,0) collide.
+# This script checks if:
+# - the numerical displacement equals the analytical displacement at a certain
+# time before the spheres separate, for instance in t = 0.05 s
+# This also implies the consistency of the results in terms of velocity
+# (and acceleration).
+# - the normal stiffness and normal damping coefficients have been calculated
+# correctly in function of the normal coefficient (en) of restitution and the
+# impact time (tc); this is a consequence of the previous condition.
+#
+# Notice that:
+# - this script only checks the displacement before the separation because the
+# analytical solution (given below) supposes that the damping term is still
+# present, when the spheres separate. This is however not true in the
+# numerical model (see source code, prevent appearing of attraction forces
+# due to a viscous component).
+# - this script does not check the tangential (or shear) behaviour of
+# the constitutive law.
+#
+
+from yade import plot,ymport
+import math
+
+
+################################################################################
+# MATERIAL
+
+rho = 2000 # [kg/m^3] density
+mu = 0.75 # [-] friction coefficient
+tc = 0.2 # [s] contact time
+en = 0.3 # [-] normal restitution coefficient
+et = 0.2 # [-] tangential restitution coefficient
+
+frictionAngle = math.atan(mu)
+mat = O.materials.append(ViscElMat(tc=tc,en=en,et=et,
+ frictionAngle=frictionAngle,density=rho))
+
+
+################################################################################
+# GEOMETRY
+
+r = 0.1 # [m] sphere radius
+
+b1 = O.bodies.append(utils.sphere(center=(2*r,0,0),radius=r,material=mat))
+b2 = O.bodies.append(utils.sphere(center=(0,0,0),radius=r,material=mat))
+
+
+################################################################################
+# SIMULATION
+
+O.dt = 1e-5 # [s] fixed time step
+v = 2 # [m/s] velocity along x-axis
+
+O.bodies[b1].state.vel[0] = -v
+O.bodies[b2].state.vel[0] = v
+
+O.engines=[
+ ForceResetter(),
+ InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),Bo1_Wall_Aabb()]),
+ InteractionLoop(
+ [Ig2_Sphere_Sphere_ScGeom(),
+ Ig2_Facet_Sphere_ScGeom(),
+ Ig2_Wall_Sphere_ScGeom()],
+ [Ip2_ViscElMat_ViscElMat_ViscElPhys()],
+ [Law2_ScGeom_ViscElPhys_Basic()]
+ ),
+
+ NewtonIntegrator(damping=0)
+]
+
+
+################################################################################
+# RUN
+
+O.run(5001,True)
+
+
+################################################################################
+# COMPARE ANALYTICAL AND NUMERICAL SOLUTIONS
+
+m = 4./3. * math.pi * r**3 * rho # [kg] mass of the sphere
+
+
+# Normal stiffness and damping coefficients according to [Pournin2001]
+meff = m/2
+kn = 2.0 * meff/tc**2 * (math.pi**2 + math.log(en)**2)
+cn = -4.0 * meff/tc * math.log(en)
+
+
+# Analytical solution of a linear spring damper system
+omega0 = math.sqrt(kn/m)
+zeta = cn / (2 * math.sqrt(kn * m))
+omegad = omega0 * math.sqrt(1 - zeta**2)
+xAnalytical = v/omegad * math.exp(-zeta*omega0*O.time) * math.sin(omegad*O.time)
+
+
+# Comparison (if ok, resultStatus is not incremented)
+tolerance = 0.0001
+
+xNumerical = O.bodies[b2].state.pos[0]
+
+if ((abs(xNumerical-xAnalytical)/xAnalytical)>tolerance):
+ resultStatus += 1
+
