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ChangeLog
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==================================================
yade-2019.02a
Tue, Jan 29 19:59:30 2019 +0100
Alexander Eulitz (9):
fix typo
fix typo
missing link replaced by short description
updated Engine names
Merge remote-tracking branch 'upstream/master'
Added MPI Developergroup
Merge pull request #54 from Kubeu/master
solved import problem of ASCII STL models
added .git config file for directly working on trunk
Anton Gladky (6):
Remove RELEASE file
Fix doctest fail with numpy 1.14
Fix doc compilation with the new sphinx
Use mathjax instead of pngmath.
Remove execution bit from some scripts
Add RELEASE file
Boon Chiaweng (7):
example files for Potential Blocks and Buoyancy routine
Local repository is outdated
Update Potential Block Examples
Update Potential Block Examples
Update Potential Block Examples
fixed the description for variables in PotentialBlocks
commented TRVAR3 in KnKsPBPhys and remove Potential Particles basic.py
Bruno Chareyre (102):
FlowEngine::getDiffusionCoeff introduced, returning throat's area/length ratio
more consistency in the 'stress' vs. 'force' semantic
some improvements following https://lists.launchpad.net/yade-dev/msg13714.html (thx Jerome)
fix compilation without gpu for older suitesparse
a latex typo in doc - blocking buildbot
Revert "Code comment in Ip2_FrictMat_FrictMat_FrictPhys: removing from the comment the erroneous 2 with respect to harmonic average expression"
fix/add some hyperlinks in doc
minor comment
theta-method for implicit integration of lubrication forces
better user control on theta method in Law2_ScGeom_ImplicitLubricationPhys, stiffness made linear, roughness!=0 improved and tested (warning: reverts 24b1cac, sorry)
An interesting new shape in Zhao et al. (2017)
suffusion modelized by Aboul Hosn et al. (2018)
better initialization of scaled densities when Newton::densityScaling is true
DomainLimiter now compatible with clumps, not just spheres
added comment to O.interactions.nth() docstring
minor inline comment
enable detachement of contacts following gap=0 in Lubrication law
inversion of integer matrix in flipCell (thx Vaclav for the hint https://github.com/yade/trunk/commit/2d7afba)
Rotations calculated with the integrator for spherical bodies if one rotational DOF is blocked
an exemple for saviing/reloading with user defined variables and functions
1-phase solver for clusters and more python wrapping
helper function for finding opposite edge
add libparmetis variant of libmetis to cmake
initialize CellInfo::index in ctor
optimized local update of clusters after each pore invasion
TwoPhaseFlow clusters: some bug fixing and more python wrapping
Merge branch 'master' of github.com:yade/trunk
bugfix in TesselationWrapper::getAlphaCaps as reported by Gerald Pekmezi
a function applying forces based on alphaShape
remove unneccesary lines
TwoPhaseFlow cluster management extended to imbibition
fix FindMetis.cmake (was looking for all variants instead of just one)
+1 paper Suhr et al. 2017
some code cleaning
returns merged clusters after pore imbibition
fix erroneuous condition in cluster drainage
Some bugfix in TwoPhaseFlow::Cluster's handling
further smallfix of clusters
saveVtk() includes boundary cells
saveVtk() include more boundary cells
final integration of bounding cells display
code cleaning and doc
remove deprecated savePhaseVtkIncludeBoundaryCells, replaced by savePhaseVtk(...,withBoundaries=True)
smallfix
fix capillary forces calculation (include revert of 8074a80a89bd451c8a) + fix a compile error for c++ < 11
fix timing.stats() runtime error when ParallelEngine has a sublist of engines (the results are still not ok)
fix some output string of timing.stats
calculate and retunr consistent timing.stats() with ParallelEngine
use numSolveThreads and numFactorizeThreads for FlowEngine::solver=4, as it is for solver=3; improve timing.stats()
mention 3SR hosting
document code and remove a cerr<<
a complete example script with spheres, grids, pFacets interactin (by Marcus Guadagnin Moravia)
augmented version of a pFacet example (thx Marcus)
re-apply: augmented version of a pFacet example (thx Marcus)
Fix inspector for PFacets/GridConnexions/GridNodes
fix compilation error when TWOPHASEFLOW is enabled with PFVFLOW disabled (now disabling PFVFLOW also disable TWOPHASEFLOW automatically). Ref. https://answers.launchpad.net/yade/+question/672510
fix compilation with vtk>8 (Thanks to Luc Oger)
starting points for thermal engine by Rob. Caulk
'#ifdef THERMAL' guards for Thermal module + fix compile error
added comment on converting State to ThermalState
update installation doc for ubuntu 18
update/highlight using yade without linux in doc
oedometer.py: remesh right after changing the boundary condition
partial fix of the display problems when PFacets are clumped together
fix broken ipython terminal (bugs.launchpad.net/yade/+bug/1604266)
improved density scaling, fixing wrong behaviour when stiffness!=0 at iter=0
updated publications and publication page
missing file 663546f (update publications page)
fix dt=0 in GSTimestepper when viscEl=True (ref https://lists.launchpad.net/yade-dev/msg14195.html)
fix bug/1794479 (doc fix)
fix https://bugs.launchpad.net/yade/+bug/1455621 (doc fix)
safer cast's in PDFEngine
doc
fix compile warning
wrapper for CGAL's incident_cells accessor (available in FlowEngine and friends)
fix return type of FlowEngine::getIncidentCell()
Revert "Changes in Python-exposed functions to accomodate the (somewhat new) list-return-type of aabbExtrema. See bug LP: #1804621"
Fix LP:1804621; revert Shop::aabbExtrema() from boost::python::tuple to std::vector<Vector3r> git:1db13fb
Merge pull request #55 from booncw/master
enable createInteraction(id1,id2) when (id1,id2) is a virtual interaction
introduce regression testing module for utils
make -j6
Merge remote-tracking branch 'github/master'
Merge branch 'master' into 'master'
replace github by gitlab in doc and sources
Merge branch 'master' of gitlab.com:yade-dev/trunk
small change on gitlab doc (test push)
remove remaining occurences of github
github->gitlab in html homepage
Merge branch 'master' of github.com:yade/trunk
Merge from github/yade
Revert "Merge from github/yade"
Merge branch 'master' into 'master'
increase make -j12
increased documentation of merge requests
CI pipeline triggered by master branch only
fix syntax in .gitlab-ci.yml
CI pipeline for merge_request's also
document the two ways for merge requests and whether they will use group runners
Merge branch 'master' of https://github.com/booncw/trunk into potentialBlocks
fix script-seesion2.py and mark psd.py OK
fix typo in index.html
Chao Yuan (4):
add a tempoary saveVtk to plot bounding cells.
-fix bug on computing fluid forces. the error computes fluidForce twice.
Merge branch 'master' of github.com:yade/trunk
temporary fix the solution of pore body radius. the previous one doesn't work if the radius of grain is smaller than 1e-5.
Jan Stránský (5):
removed utils.UnstructuredGrid
fixed some warnings for sphinx doc compilation
added publications
Making doc of Body.intrs() clear to return real interactions
added brazilian splitting test example script
Janek Kozicki (35):
Fix all compilation warnings
Fix last compilation warning
Fix compilation errors with CGAL 4.11 (again), guys please use Tri.locate(CGT::Sphere(…)) and ->point().point()
Update .mailcap
Small improvement in SerializableEditor.py, it will now detect types starting with std:: or boost::
Initial idea for fixing CGAL 4.13 interface changes.
fix typo
Add info about how to push a non-master branch into yade-dev
Checked first 20 examples. Fixed 2. Created full list examples/list_of_examples.txt to track progress.
Partial fix of postProcessValidMaurin2015.py
Fixed postProcessing_sedim.py; added in list_of_examples.txt whether the example is explained inside the script.
Checked next 25 examples. Added some explanations or very small fixes in 8 examples.
Checked 10 more examples.
Check 24 more scripts, fix 2.
Check 12 examples. Fix 2.
Check 8 more examples
Checked 17 more examples. Didn't fix the 8 broken ones.
Checked 18, fixed 2
Checked 17 more examples
Check 27 more examples
Checked last 25 examples. Conclusion: 215 examples, 46 are not working at the moment. That is 21% of examples are broken.
Fix bug#1813229. Class Inheritance graphs in Yade.pdf now have dpi=300 and larger font.
I tried the -DENABLE_POTENTIAL_BLOCKS=ON -DENABLE_POTENTIAL_PARTICLES=ON examples. They start and seem to run, but still do not work.
Oops, has some merge conflicts
I tried PotentialBlocks once again. I am still suspicious about whether those examples work.
Fix error GUI → Display → Gl1_CpmPhys : UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 87
Adding Gl1_PotentialParticle().store=True to example file seems to fix the display issues. But there must be a reason why it is false by default?
Comment out last remaining //TRVAR3(…) which was spamming the terminal.
Fix indentation in list_of_examples.txt
Checked all examples in doc/sphinx/tutorial.
Walked again through all examples to identify the source of each SIGSEGV/SIGABRT segfault.
Notes about what I achieved when trying to make this line work: 'from esys.escript import *'
Two of FEMxDEM scripts started to sort-of work: biaxialSmooth.py and retainingSmooth.py
Added missing references to my articles using yade. Also my first Quantum Mechanics paper ;)
Maybe embedding videos with https will make them work on the website?
Jerome Duriez (44):
Ip2_FrictMat_FrictMat_FrictPhys doc: correcting typo (see previous commit comment)
Code comment in Ip2_FrictMat_FrictMat_FrictPhys: removing from the comment the erroneous 2 with respect to harmonic average expression
Capillary scripts: minor changes in writesCapFile
Code comment in FrictPhys: we are adding compliances, I do not think we average them. See also https://github.com/yade/trunk/commit/1f013766d191a0e931d3c1653242d22f28e36dd5
Capillary scripts: minor correction in writesCapFile.m affecting the search for maximum suction when contact angle # 0
Capillary scripts: improving search for maximum suction in writesCapFile.m
Typo corrected in makeCloud() doc
Doc (Programmer s manual) typos corrected
FileGenerators: removing deprecated CapillaryTriaxialTest and CohesiveTriaxialTest. Fixing bugs https://bugs.launchpad.net/yade/+bug/1625850 and https://bugs.launchpad.net/yade/+bug/1764753
Doc: Timing section of Programmer manual. Correcting typos and small changes in wording regarding instantiation which is already done in the mother classes (and does not need to be redone in the Engine/Functor to measure)
Bibtex entry for the 2nd YADE workshop proceedings. Thanks to all yade-dev authors !
Shop::growParticles(), fixing bug https://bugs.launchpad.net/yade/+bug/1767601. There was some interaction access before checking the real nature of interactions, leading to crash with erased bodies
Doc typo corrected
Programmer s Doc: removing Debian packaging section. Fixes bug LP:1773337
Doc: updating my affiliation
+2 journal papers
+1 journal paper (Mede et al.)
Doc typo
InteractionLoop doc typo and small precisions
Merge pull request #52 from jandepue/master
Code cleaning after previous commit about a new matchmaker in CohFrict model
Doc
Correcting previous doc commit (orientation attribute for utils.box())
Doc typo
Docstring typo in pack module (better sphinx output now)
Doc typo
Removing deprecated pack particleSD*()
Doc typo
Merge branch 'master' of github.com:yade/trunk
Adding some kind of warning in SPH examples README
State doc typo
Doc VTKRecorder: typo and minor changes for bstresses
VTKRecorder bstresses: removing useless code for sorting principal particle stresses: Eigen already does it
Shop::aabbExtrema() from boost::python::tuple to std::vector<Vector3r>
Including new type (from -1 commit) in aabbExtrema doc
MeasureCapStress: fixing bug LP: 1764424 and change of attribute names
Doc typo (McNamara doi)
Formulation doc typo (wrong superscript for \omega somewhere)
Publications: adding full bibliographic details for one paper
Doc for compilation options, some sync between the doc and CMakeLists.txt. See https://lists.launchpad.net/yade-dev/msg14108.html
Moving isInBB from py/_utils* to pkg/dem/Shop*
Doc typo in URL link (correcting 0a292779)
Changes in Python-exposed functions to accomodate the (somewhat new) list-return-type of aabbExtrema. See bug LP: #1804621
Doc for pack module: fixing broken links
Luc Scholtes (2):
Back to previous configuration (Timos's version) - Robert's add ons commented - More testing needed
add the possibility to distinguish cracks from matrix and joint interactions in Paraview
Robert Caulk (48):
throw error at user for trying to useSolver=4 with multithread=False
Add acoustic emission collection algorithm to JCFpm. Add acoustic emission post processing tools to VTKRecorder.
Add guide for simulating acoustic emissions
clean up installation and GPU doc
convert pdf images to png for AE guide
fix doc build failure
fix figure web sizes
edit concrete example to aboid ZeroDivisionError
revert doModes back to original value
Add eventnumber post processing category for acoustic emissions alg
move trickperm to fix broken blockhook
add ability to artificially correct cell volumes based on a desired porosity (EXPERIMENTAL)
add functionality to collect start time of acoustic emission event
clarify citation, equations, images for acoustic emissions tutorial doc
remove DFNFlow from default compilation
Parallelize mesh interpolation
open useSolver=4 to singlethreaded operation
fix bug with singlethreaded GPU flow solver
add ability to measure some FlowEngine and CHOLMOD timings
Merge branch 'master' of github.com:yade/trunk
set openblas_num_threads = flow.ompThreads
Basic functionality for fixing triangulation and updating linearsystem with trickPermeability
comment out update positions
add functionality for resuing CHOLMOD ordering (avoid unnecessary CHOLMOD analyzing)
erase random comment
Fix typo
Add ifdef for LINSOLV=OFF in FlowEninge and force TWOPHASEFLOW dependency on LINSOLV=ON
advection function added to flowengine, thermal properties added to cells
Merge remote-tracking branch 'refs/remotes/origin/master'
remove unnecessary variable initializations
add functional conduction engine
consolidate thermal engine, fix #ifdefs
Merge branch 'master' of https://github.com/yade/trunk
add thermal mechanical coupling, enable individual control of advection or conduction
add ability to set conduction boundary conditions
add start of thermal-mechanical fluid coupling
add full thermomechanical fluid coupling, automatic timestepper, refactor, clean
fix indentation
improve readability and add ability to decouple forces in flowengine
adapt thermal state info and engine for compatability with special states (e.g. jcfpm). Add cmake flag for thermal engine.
add Yade Technical Archive to website and doc
change links for yade tech archive to /publi, add yade tech archive references to reference page
#ifdef factorexists
update YTA hyperlinks
add comma
update YTA hyperlinks
Update YTA tutorial refs
Fix memory leak in FlowEngine
William Chèvremont (72):
hide debug messages
Merge branch 'master' of https://github.com/yade/trunk
Merge branch 'master' of https://github.com/yade/trunk
Merge branch 'master' of https://github.com/yade/trunk
Physics update in Lubrication law for bodyStressTensor
Merge branch 'master' of https://github.com/yade/trunk
Merge branch 'master' of https://github.com/yade/trunk
add stresses calculation to implicit lubrification
Merge branch 'master' of https://github.com/yade/trunk
Fix normal lubrication
Merge branch 'master' of https://github.com/yade/trunk
Fix lubrication laws
Merge branch 'master' of https://github.com/yade/trunk
Fix lubrication compile error
Fix compilation error: missing include
ccache doesnt support -save-temps
Add dynamic stress calculation alone
Delete LubricationPhys, add stress calculations for each component, change resolution method
Missing replacement of EIGENSPARSE_LIB to CHOLMOD_LIBS (see commit f9cac61952163e0897942e596fa5bb24a55c9f5d)
Fix time stepper stiffness
Add scripts replacement tags
Modification to OAR launch script
Modification on lubrication's laws
Adding possibility of saving a dict of parameters
add oar-properties support
fix constrain orders -oar
Change lubrication calculation structure
Fix Dynamic stress calculation
add normal viscosity for timestepper
Encapsulation of resulution method into functions
Change some default values
Give a default value to RealName (getpwuid(geteuid()) fail on some clusters but not so critical)
Add Newton-Rafson resolution method
Add newton-rafson method with nonlinear contact
Fix compile cast error
Add NewtonRafson-Exponential resolution method
Nonlinear contact only belong to contact part
Documentation improvement
Move non-normal calculation to a function (help for inheritance purposes)
Fix doc warnings
Switch to implicit resolution
Fix warning
Add stress calculation
Fix OAR launchscript bugs
Add log-calculation of shear and torques component
Switch to log-shear resolution
Fix DLVO equations
Fix substepping distance
Reduce warning verbosity
fix script path for logfile
Fix Electrostatic + lubrication
Add dichotomic method for resolution
End of Dichotomy implementation, renaming
Fix compile error
bugfixes
Add VdW cutoff length
Add Stress PDF for lubrication
Switch to template implementation for PDF
Fix buildbot error?
PDFEngine creation
Move PDF to new file, exemple for lubrication
Add distance, velocity and intrs PDF integrator
Add Distance, Velocity and Intrs calculation for Lubrication
fix compile warnings
Add default data for PDFEngine
Doc for yade-oar
Check for initial proble
Fix NaN function problem at initial point
Regula Falsi
Code refactoring
Fix starting point
Merge branch 'master' of https://github.com/yade/trunk
jan (1):
Added frictionAngle Matchmaker to cohesive frictional contact law (based on Frictphys) see https://answers.launchpad.net/yade/+question/670376
raphm1 (15):
HydroForceEngine: Re-organize fluidResolution to make it clearer. Remove lines and tab the text according to the different loop Remove the subfunctions which are not usefull anymore Uncomment the calculation of taufsi
HydroForceEngine: fluidResolution modifications Modify the grid definition and the extrapolations of variables in order to fit exactly the staggered grid and the averaging performed. Modify the example scripts accordingly. This modification fixes former errors in the formulation of the fluid resolution. Change the variables name to be consistent with the future documentation
HydroForceEngine: error in the pressure term + validation Correct an error in the pressure term of the fluid resolution Introduce a fitting coefficient in the wall friction Adapt the validation script to the mesh
HydroForceEngine: add validations scripts Add a script to reproduce the experimental comparison performed in Maurin et al 2015 Add a script to reproduce the case r2d6s2 of Maurin et al 2016 Add post-processing scripts to extract corresponding figures
HydroForceEngine, fluid resolution: add the possibility to impose a fluid velocity at the top of the sample.
HydroForceEngine: modify the example folder organisation
HydroForceEngine examples: modify the fixed bottom generation
HydroForceEngine: add an example script of laminar shear flow over a granular bed
HydroForceEngine: add a new effective viscosity modelling
Add references
Fix error in the previous commit in references
Add a documentation page for HydroForceEngine
second part Add a documentation page for HydroForceEngine
HydroForceEngine: correct the viscous contribution Modify the viscous contribution in the fluid resolution, in order to account for the fact that the closures for the viscous stress tensor should be written as a function of the total (fluid+solid) shear rate tensor. As a consequence, the fluid viscous contribution are multiplied by the fluid volume fraction at the square, and the second member includes a contribution from the solid phase. Also, the poiseuille validation script has been very slightly modified to account for recent code modification
HydroForceEngine: add a point particle averaging function
remche (14):
adding gitlab-ci
4 cpu for build
16 cpu for compilation
more complete ci
disabling save temps
clean build for artifact and relative path for install
make and install in the same job
fix install dir
test doc generation
fi xvfb-run
fix depth for xvfb-run
uploading pdf and epub doc to pages
Adding DISABLE_SAVE_TEMPS flag to Cmake
doc: fix jquery for searchbox
==================================================
yade-2018.02b
Tue, Feb 20 18:55:30 2018 +0100
Anton Gladky (4):
Remove RELEASE file
Do not globally import polyhedra_utils in ymport.py
Simplify and fix the checkPolyhedraCrush
Add RELEASE file
Bruno Chareyre (1):
fix cmake warning + effectively enable TWOPHASEFLOW
Janek Kozicki (3):
Update .gitignore and .mailmap
Fix warnings that I have during compilaation.
Initial fix for cgal 4.11. There are some things still to check:
Jerome Duriez (4):
Doc: typo (missing parenthesis) in Ig2_Sphere_Sphere_ScGeom
Doc: precising IPhysFunctor docstring
Doc: typo in Programmer s manual
Doc: other typos in Programmer s manual
Robert Caulk (2):
Fix DEM-PFV-check.py failure. Enable CPU usage of direct cholmod solver (useSolver=4)
Add support for older versions of SuiteSparse
==================================================
yade-2018.02a
Wed, Feb 7 20:06:30 2018 +0100
Anton Gladky (15):
Remove RELEASE file.
Initialize gui in IPython 5.
Add dependency on python-pyqt5.qtsvg.
Fix PDF-compilation with sphinx>=1.4.9
Remove comented lines in CMakeLists
Test commit number two.
Do not enable LINSOLV if CGAL not found
Fix missing AND operator in prevoius commit
Extend polyhedra breakage model by Mohr-Coulomb-Weibull failure criterion.
Add examples for the PolyhedraBreak model
Add one more Yade-Paper
Update .gitignore
Make newly added labels consistent with other labels.
One more thesis, where Yade is mentioned
Add RELEASE file
Bruno Chareyre (15):
Fix https://bugs.launchpad.net/yade/+bug/1666339 (thx Robert)
+5 journal papers
+2 journal papers
+ Christian Jakob's PhD in references
Put brackets in the right place (thx Robert).
+4 journal papers
1+ journal paper by V. Lapcevic
Add editor to Yade workshop proceedings (me!)
missing comma (sorry)
turn ERROR into WARNING when ISCollider does not find spheres to determine verletDist
+2 journal papers
+2 journal papers
+11 conference papers
add missing year in a bibtex entry
Fix kineticEnergy() for clumps
Chao Yuan (6):
add porosity in cell info.
fix compile error.
add functions to get pore throat radius (by cells or spheres).
-split computeEffectiveRadius() for obtaining reff by pos and radius; -clean redundant functions.
-fix setPoreThroatRadius
-add setPoreBodyRadius.
Francois Kneib (1):
Fix typo in installation.rst doc.
Jan Stránský (7):
fixed a typo in micro-stress example
replaced L3Geom by ScGeom in tutorials
Added subengines of CombinedKinematicEngine to labeled engines
fixed a bug in ScGeom::getIncidentVel with avoidGranularRatcheting=False and O.periodic=True
Updated Body::intrs doc, fixed typo in comment
fixed a bug in ymport.UNVReader
fixed one Polyhedra python method name
Jerome Duriez (9):
Articles .bib entries: fixes https://bugs.launchpad.net/yade/+bug/1671045, plus update of entries data
capillaryLaplaceYoung scripts: update of reference labels
+1 master thesis
A new post-processing engine to measure capillary stresses using alternate expressions than getCapillaryStress()
Implementation improvement of new MeasureCapStress engine
JCFpm model: code comment precised (https://answers.launchpad.net/yade/+question/644244)
-1 check test (regarding NormalInelastic contact law which is about to be erased)
-1 contact law (Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity and other NormalInelasticPM classes)
Typos corrected in installation.rst
Martin Haustein (1):
Add constant volume deformation engine.
Robert Caulk (4):
Editorial change
fix typo
Fix typos
Roll breakOccurred comments back 1 commit
T Sweijen (12):
Dynamic version of two-phase flow,interpolation of saturation field when meshing, merging of tetrahedra to find pore units
OMerge branch 'master' of https://github.com/yade/trunk
provide access to per pore partial solid surface
update of Dynamic Two-Phase Flow engine, removing old definitions, update comments, and added several averaging procedures for water pressure
Function to track deforming pore units and to couple this to dynamic two-phase flow + cleaning of functions
Minor fix for updating volume change
fix for savePoreNetwork function - to avoid odd locations of cells along boundary
fix of comments and cleaning up of redundant lines. Also, inclusion of initial and boundary conditions for dynamic imbibition
Fix for mergeCells() function, to allow for using it more than once
Update of initial conditions to allow for primary and secondary drainage/imbibition. Addition of compatibility check of boundary conditions. Removing some redundant functions.
Fix in TPF Engine for simulations with Deformation + optimalization for TPF + deformation simulations, without swelling
update of soluteFlowEngine, including a fundamental fix in equations and a function to export average concentration
William Chèvremont (25):
Adding Electrostatic interaction
Adding Electrostatic interaction (forgot cpp file)
Fix the electrostatic law
Merge branch 'master' of https://github.com/yade/trunk
Correction of ElectrostaticPhys
Adding lubrication force w/o FlowEngine
Merge branch 'master' of https://github.com/yade/trunk
Merge branch 'master' of https://github.com/yade/trunk
ElectrostaticMat derive from CohFrictMat instead of FrictMat
Merge branch 'master' of https://github.com/yade/trunk
Fix lubrication laws
set more realistic default values for ElectrostaticMat
Lubrication can process other physics
Adding yade-oar and Lubrification resolution by implicit method
Revert "Adding yade-oar and Lubrification resolution by implicit method"
Revert "Revert "Adding yade-oar and Lubrification resolution by implicit method""
Merge branch 'master' of https://github.com/yade/trunk
fix lubrication
fix plot Matrix3 suffix (yz instead of yx)
Merge branch 'master' of https://github.com/yade/trunk
Fix CMakeList
Test
Fix warnings
Debug lubrification
Insert other resolution method
bchareyre (59):
fix the flipCell() function
fix compile error
flipping periodic cell -> small/doc fix
move PBC example scripts
cleaning examples
documentation on changing the boundary conditions in FlowEngine and derivatives
Robert Caulk's guide to cloud computing inserted in doc
return a consistent set of constrictions in the periodic case (some constrictions were previsously skipped inconsistenty)
re-apply the fix of rev 26efbec to getConstrictionFull()
fix a compile warning
fix an indentation problem in shinx document - hopefully fixing the buildbot
fix unicode warning (documentation build)
add a reference url
fix compiler warning
small fix in getConstriction() + a typo
new logic for interating on facets in periodic triangulations (following ref. Rev.26efbec and followers)
new data 'crackArea' added to DFNFlow cells and updated automatically - first step toward solving the artificial compressibility of fluids in cracks
#define DFNFLOW commented out
small updates in doc, fixing compile errors and some warnings
add exemple script for two-phase flow with 2PFV technique, related to Yuan and Chareyre (2017)
extended version of ForceEngine with its own fluid solver (by J. Chauchat)
move HydroForceEngine to independent source files.
Minor changes in authorship and inline comments
Critical bugfix for collision detection in periodic boundary conditions. Bounds lists were left partially unordered, then some interactions were never detected (my toughest yade debugging until now).
Minors & cosmetic.
fix feature NewtonIntegrator::densityScaling
Introduce a tolerance on overlap determination (in periodic BC only), avoiding false negative due to round-off errors. (usage in a separate commit).
A simpler and faster version of spatialOverlapPeri. Only one call to floor(), ~20% speedup for ISCollider::action. Tolerance introduced to fix detection failures.
Keep the values of sorted bounds in the [0,size] range in ISCollider.
small scale optimization in ISCollider
Fix collision detection again (amending commit c7c8e6f62d452c8). Don't move bounds below the starting point of the sort, else partial (only) ordering can occure.
Don't start blinking the 0-body when opening inspector + make it possible to un-highlight before/after closing the inspector by selecting empty space.
Fix miscommit in d2211bd747d74eaea569ac88e.
remove a function that was declared but undefined (leading to runtime error)
cite recent reference on timestep
TwoPhaseFlowEngine::getNeighbors now returning less than 4 neighbor cells if some of them are infinite (normally only one)
a function + python wrap for invading one single pore and updating the clusters
fix cluster invasion/update (thx Son for spotting the bug)
fix doctest's target following b5ca352
fix doctest in addData (re-apply c011decc36)
fix doctest indentation (after 36c016bd)
TesselationWrapper wrapping CGAL's AlphaShapes for defining an alpha-contour
remove function definitions from FlowEngine.hpp
preliminary version of 'extended' alpha shape contour
further extension and debugging of alphaShape code
nearly working version of the extended alpha-contour
small fix
proper calculation of alphaCaps areas in TesselationWrapper
If FlowEngine::meshUpdateInterval<0 do not update the mesh at fixed intervals
fix a compile warning - probably leading to undefined behavior
apply d71813b for the periodic flavor of FlowEngine
re-insert the comment on Qt4->Qt5 since it may still help (partial revert of 1c06b6ad9d2)
Remove the declaration of (redundant and undefined) FlowEngine::currentTess, while there is already Network::currentTess. Fix https://bugs.launchpad.net/yade/+bug/1732210.
Use a relevant upperbound (i.e. 0.5*period) for the the maximum body size in periodic boundary conditions.
Update the position of the clump members relative to the clump itself ("local" coordinates) when applying growParticles(). It is no longer necessary to perform additional operations (updateProperties()) after growing clumps.
make checkClumpHopper.py less time demanding
fix bug/1291977 and a typo
fix some compile warnings in TwoPhaseFlowEngine
enable TWOPHASEFLOW by default
jduriez (15):
Email address changes
Capillary script solveLiqBridge.m: change in attributes order (with small consequences), plus other minor changes
Capillary scripts: removing one useless test, and including commented time measurement commands
Capillary scripts: Introducing .py versions for 2 (out of 3) .m files. Plus minor change in one .m file
Doc: precising Collider.avoidSelfInteractionMask
+2 book/proceedings chapters (and formatting changes)
Doc of Shop::aabbExtrema precised
Doc typos and small improvements in VTK post-processing descriptions
Small doc changes in TriaxialStressController.particlesVolume and porosity
Doc: minor change in package installation (distro name)
Doc: typo in user manual
Misleading comment removed in UnsaturatedEngine.cpp
Doc: typo correction in TriaxialStressController.stressMask
grids examples: moving qt.View() at the end of the scripts so that the window view is correctly scaled with respect to the model
Doc of Ig2_Sphere_PFacet_ScGridCoGeom updated: replacing inexistant ScPFaceCoGeom with ScGridCoGeom, and Facet with PFacet, fixes 4. of https://bugs.launchpad.net/yade/+bug/1746037
luc scholtes (6):
update of the JCFPM particle model with new or adapted functionalities to record number of cracks and associated released energy. An example script will be provided.
add possibility to define residual friction angle (broken contacts) different from friction angle (bonded contacts)
some cleaning and clarifying of crack aperture calculation
update of file. mistakes in previous commit
update due to mistake. Thank you Robert
update due to mistake. Thank you Robert
raphm1 (10):
HydroForceEngine: add an optional input parameter to account for convective acceleration The input convective acceleration term take the form of a depth dependent vector
yade-article.bib: add a journal paper
Add proceedings
Add two functions getStressProfile_contact: to evaluate the stress profile considering only the contact contribution getDepthProfile_center: to evaluate solid depth profile (solid velocity and volume fraction) considering particles as points
Fix error from commit e4f601d
Add 2 references and 1 paper
HydroForceEngine: update the 1D RANS fluid coupling Modify the formulation of the fluid resolution in order to merge it with the existing variables of HydroForceEngine. Fix errors in the fluid momentum balance resolution. Clarify the mesh definition. Evaluate all the components necessary to solve the equations inside the fluidModel function. Introduce the possibility to account for fluid lateral wall friction in the equations. Make it possible for the user to access only the fluid resolution without introducing any particles or launching a DEM simulation. Update the documentation.
HydroForceEngine: new examples and validations Introduce a new sedimentTransport script, which make use of the fluid coupling (1D RANS) Complete the sedimentTransport example script and add a post-processing example. Add validations for the fluid resolution without particles, considering logarithmic law and poiseuille flow. Add a file commenting the different examples and validation scripts.
HydroForceEngine: small modifications
HydroForceEngine: fix errors in the fluid resolution
remche (4):
Fixing clang compilation
Adding path for CGAL ans GMP include dir to cmake (for exotic installations)
Merge branch 'master' of https://github.com/yade/trunk
Adding the correct include dir for CGAL
robcaulk (15):
added tmux command tip
Fixed bug with multithread+compressible flow and addressed backgroundAction() FIXME for eigenSolve()
fixed inheritence problem when LINSOLV=OFF
Added option to let new bond breaks in JCFpmPhys control retriangulation in FlowEngine
add fracture interpolation functionality
GPU accelerated PFV solver
GPU acceleration guide
Avoid compiling suitesparse GPU solver if -DCHOLMOD_GPU=OFF
improve GPU doc
Merge branch 'master' of github.com:yade/trunk
improve GPU acceleration guide
add the ability to threshold trickpermeability to 2 or more facets, default behavior should remain same as before this commit
fix variable naming inconsistencies
Merge branch 'master' of github.com:yade/trunk
fix multithreading issue with imposed fluxes
williamchevremont (1):
Typo
==================================================
yade-2017.01a
Thu, Jan 19 22:07:25 2017 +0100
Anton Gladky (20):
Remove RELEASE file.
Add some notes about how to make releases.
Make Yade compatible with VTK7.
Use C++11 constructions for InteractionLoop.
Optimize using of ndarray.
Partly fix webpage help show. LP:1598174
Final fix for LP:1598174
Add missing dependency on python-pyqt5.qtwebkit.
Fix load/save in GUI-QT5.
Drop unused typedef.
Disable LAW2_SCGEOM_CAPILLARYPHYS_Capillarity1 by default.
Remove some deprecated scripts.
Increase the size of force container.
+1 paper.
Provide a proper functioning with IPython5.
Add -fext-numeric-literals to fix FTBFS against boost_1.62
Fix yade with IPython5.
Update distro names in documentation
Add missing header include <csignal>
Add RELEASE file.
Bruno Chareyre (12):
+2 articles (thanks to Bettina Suhr)
+ 1 proceedings (thanks to Bettina Suhr)
Update citing_yade.bib
revert the revert ca0e29ac57
list authors of the doc as in doi:10.5281/zenodo.34073
a note on using distcc and ccache
minor editing of installation page
Master thesis Morales2012a
Introduce Network::surfaceSolidThroatInPore() for partial solid surfaces per half-throat
make the recursion conditional for invasion in multiphase flow
push a file missing in commit e91ff135b7
Yade bibtex: "and others" invalid for less than 9 authors
Chao Yuan (4):
Add cell label for phase cluster. NW-res label 0, W-res label 1, disconnected w-clusters start from 2. label can be saved in savePhaseVtk.
fix comment on label.
clean UnsaturatedEngine, move all functions to TwoPhaseFlowEngine.
Revert DryingEngine.
Francois Kneib (1):
Fix O.engines in examples/cylinders/cylinderconnection-roots.py
Jan Stránský (11):
fixed a small bug in shear force computation in CPM model
Added PolyhedraSplitter example
Changed L3Geom to ScGeom in tutorial example scripts
fixed a minor compilation issue in ConcretePM
Fixed call of _utils.interactionAnglesHistogram with default arduments
making all Law2::go virtual
Matrix_computeUnitaryPositive, changed computeThinX to computeFullX flags
User's manual, added how to visualize force chain in Paraview
UnstructuredGrid: fiexd little bug in manual setting of facet position from vertices
added pack.inHalfSpace and pack.inConvexPolygon + example script
fixed another little bug in utils.UnstructuredGrid
Jerome Duriez (11):
Doc clarification for TriaxialStressController.externalWork (http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg12083.html)
Doc of utils.readParamsFromTable() hopefully improved
Friendlier BibTex entries for 2015 doc. To avoid Smilauer and et al in manuscripts
Doc Getting help section updated to reflect current practice
Including interface orientation data in CapillaryPhys code
Capillary scripts commit (http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg12103.html). Located in a new examples/capillaryLaplaceYoung folder intended to illustrates capillary Law2. With one new simulation script example and another old one, moved here
Typo and minor corrections of previous capillary commit
Capillary law2: erasing when necessary sphere-non sphere interactions (bug LP: #1628273) + minor changes
Capillary law2: restricting test shape. Plus minor change in capillaryLaplaceYoung/README text file
Doc: small updates in PartialEngine and KinematicEngines
References .bib files: including new entries
Raphael Maurin (4):
HydroForceEngine: add a condition to ignore particles fixed on the sideWalls.
Add an example for the use of HydroForceEngine
HydroForceEngine: new fluctuation model for the example script + small correction Add new simple discrete random walk fluctuation model, to be used with the new example script fluidizedBed.py Change the condition for applying the fluid force from p>0 to p>=0, which is more appropriate
Add two example scripts for the use of HydroForceEngine One simple example to get familiar with the application of buoyancy (buoyantParticles.py). One example simulating a fluidized bed configuration to get familiar with both the application of a fluid velocity profile and of turbulent fluctuation with the DRW models (fluidizedBed.py)
bchareyre (19):
fix invalid pointer, thanks Jerome (https://lists.launchpad.net/yade-dev/msg12791.html)
(doc) clarify the meaning of TriaxialStressController::externalWork
fix 1 compile warning
reordering bib references
remove latex/multicolumn from sphinx conf.py (compile error on some systems)
Law2_ScGeom_CapillaryPhys_Capillarity: cache getClassIndex() for use in a loop
fix wrong access to a Network::boundary by index
FlowEngine: enable the definition of continuum scale permeability independent of particle sizes
Introduce DryingEngine (two phase flow with convection in one phase)
Implement Darcy scale permeability in FlowEngine, introduce alphaShapes (commented), some code cleaning and smallfixes
(FlowEngine) optionaly include/skip bounding cells when calculating the average pore pressure
fix negative volumes issue in triangulation cells, consistentlyy remove the includeBoundary option (a workaround) in averageVelocity
TwoPhaseFlowEngine: better integration of fluid clusters
merging PhaseCluster code with r3975
fix compile warnings
small optimization in Clump::updateProperties
update phaseCluster attributes: volume, interfacial area, etc. + various smallfixes in the cluster labelling
further improvement of the cluster labeling in multiphase model
2PFLOW engine: remove useless int from getInterfaces()'s parameters
booncw (2):
Pushing Potential Blocks based on CWBoonEtAl2012 Computers&Geotechnics/CWBoon 2013 PhD thesis, but using CLP as linear programming Solver. CLP can be downloaded from Synaptic Package Manager: coinor-clp, coinor-libclp-dev, coinor-libclp1, coinor-libosi1v5. To enable this, set ENABLE_POTENTIAL_BLOCKS to ON in CMakeLists.txt"
revising Potential Blocks to the latest version to run slope analysis
raphm1 (1):
ViscoelasticPM : fix resolution problem in find_cn_from_en function Change the value of the initial perturbation for the resolution of the equation to obtain the damping from the restitution coefficient. Allows for a much wider range of resolution in terms of mass, stiffness and restitution coefficient. Put a limiter to avoid division by zero and force the loop to print the warning message if "error" goes to nan (no warning in these cases previously)
==================================================
yade-2016.06a
Tue, Jun 14 20:30:53 2016 +0200
Anton Gladky (88):
Remove release.
Clean some unused macroses (old wm3-stuff)
Remove some global headers
Raise minimal boost version to 1.47
Add -DNDEBUG if compiling in release mode
Tiny code refactoring
Clean some warnings and old stuff.
Return removed header back.
Fix warning in newer matplotlib.
Drop old commented stuff in python-scrips.
Remove flags and preSteps from scene
Remove deprecated findBoundDispatcherInEnginesIfNoFunctorsAndWarn
Remove PISC_DEBUG.
Fix typo in installation sections of doce. Thanks to Jan.
Export normal and viscous part of the visco-elastic contact
Remove confusing part in installation part of documentation regarding Qt5.
Fix typo in CMakeLists
Tiny updates of examples of LudingPM.
Fix compilation warnings.
Update formatting in SpherePack
Fix an order of calculation of c in SpherePack
Fix some compilation warnings.
Fix cappitalization typo in Lapack (case-sensitive in this case).
Respect VTK6 in PotentialParticles.
Add .travis.yml for CI.
Remove version restriction on sphinx.
Use trusty as build-env.
Add -y parameter to apt-get install.
Fix numpy import on travis.
Fix segfault during save/load of CapViscModels
Add one more check-script (capillary models)
Fix typo in check-script.
Fix crash in Ig2_Facet_Polyhedra_PolyhedraGeom
vtkExporter: increase number of leading zeros to 8
Move implementation of methods of ForceContainer in cpp.
Split implementation of ForceContainer in parallel and serial.
Add zero-forces to the youngest body after simulation load. Closes LP:1560171
Drop parallel execution in replaceByClumps. Closes LP:1559098
Add import of polyhedras from the file.
Add an opportunity to shift, scale and rotate imported polyhedrons
Minor fixes in Polyhedra_splitter.
Fix division by zero crash in Polyhedra
Add CGAL_DISABLE_ROUNDING_MATH_CHECK, -frounding-math when CGAL is enabled.
Fix some formatting issues.
Non-invasive fixes in polyhedra_splitter.
Get max-min coefs in polyhedra_splitter simpler.
Use tuple as a parameter for SplitPolyhedraDouble
Add check script for polyhedra crash.
Use explicitly -DNDEBUG instead of CMAKE_CXX_FLAGS_RELEASE
Check isnan in some coordinates before calling CGAL.
Minor formatting fixes in Polyhedra.
Add check-script for save/load of clumps.
Disable checkPolyhedraCrush. It is unstable now.
Fix checkPolyhedraCrush
Remove polyhedra_utils import from "ymport"
Add prefix std:: to isnan and isinf.
Update checkPolyhedraCrush
Update files for ppa-infrastructure.
Undef NDEBUG in all polyhedra files.
Add pause for checkSaveLoadClumps to escape race condition.
Use variadic arguments in DynLibDispatcher.
Fix crash in polyhedra, if maxFs=0.
Fix checkPolyhedraCrush (remove qt)
Remove unused functionality in Dispatcher.
Set Qt5 by default.
Add mathcmaker for normalCohesion and shearCohesion.
Split QGLViewer.cmake on qt4 and qt5 versions.
Add .gitattributes to ignore line endings.
Migrate buildppa to python3.
Replace some "#define"(s) by functions.
Remove some machine-specific items in documentation.
Add unit test for matchmaker.
Replace vector by unordered_map data structure in Matchmaker.
Minor fix in documentation.
Replace some "defines" by functions.
Remove numpy.hpp.
Fix bug in polyhedra_splitter.
Some cosmetic fixes in core-files.
Enable C++14.
Revert 2dc99 and ed8dcb.
Use unordered_map instead of map for MapId2IntrT
Use unordered_map only for Boost >= 1.56
Back to C++11.
Revert using unordered_map in Body.
Scale mass and inertia in spheresModify.
Reduce size of flags in Bounds of InsertionSortCollider
Fix bug in MatchMaker.
Add RELEASE file.
Bruno Chareyre (16):
add labels to default engines for easier showcases
fix ambiguous syntax, fixing https://bugs.launchpad.net/bugs/1514477
introduce 2nd edition of the documentation and contact for consuting (in homepage)
update the webpage about citation with 2nd edition, add 1st edition as an external reference, update pdf metadata
fix one DOI of the 2nd ed. documentation
Add missing toctree's for the citable book versions
fix typo in installation page
fixed DOI
fix some hyperlinks pointing to the old geo.hmg.inpg.fr
declare mask attribute for FlowEngine, fixes a compile error
use FlowEngine's mask consistently
implement standalone plastic-shear energy counter in CohesiveFrictional Law2
define constrictions with consistent cell's ids (see https://answers.launchpad.net/yade/+question/288118)
fix a compile error
update boost version in prerequisites (installation page)
Documentation: include unp in the equations of Law2_ScGeom6D_CohFrictPhys_CohesionMoment
Burak Er (1):
Implement deformable elements
ChiaWeng Boon (1):
Commit Potential Particles: non-spherical particles for DEM
Francois Kneib (8):
TesselationWrapper : add a security that prevents user to access the strain tensor of a particle (aka deformation) outside its boundaries.
Fix a tensor access in local displacement calculation.
Fix a bug in Tesselationwrapper: one of the bounding planes was not rightly positionned.
Fix in TesselationWrapper: allow the tesselation to compute right triangulation in the boundaries of a periodic boundaries conditions simulation.
Add 5 setters for bodies pos,vel,ori,angVel,color to workaround the memory leak bug when assigning attributes from python (see https://bugs.launchpad.net/yade/+bug/1041084). They are not supposed to stay in the code for a long period (remove them when the bug is solved), but are useful in sims that massively change values of python/c++ binded attributes.
Simplify one line in TesselationWrapper.
Fix the debug build that failed to compile due to a mistake in pkg/dem/Polyhedra.cpp
Fix the inspector GUI for Qt5, thanks to Mark S. Bentley.
Jan Stránský (30):
Merge pull request #47 from booncw/master
Potential particles modification
Merge branch 'master' of github.com:yade/trunk
Potential particles modifications
added forgotten file from previous commit
Modified python interface for O.forces.addF(...,permanent=True) and addT(...,permanent=True)
fixed some warnings during docs build
Added frictAngle MatchMaker for Ip2_FrictMat_CpmMat_FrictPhys
set b.aspherical=True in utils.polyhedron and utils.tetraPoly
Polyhedra modification
Added a material model for mortar layer
Polyhedra.setVertices improvement, preventing memory leaks (question #290947 and bug #1570679)
Interaction::reset explicitly resets also its functorCache
Fixed a strange bug in Law2_PolyhedraGeom_PolyhedraPhys_Volumetric and shearForce
Added useRef parameters to VTKExporter.exportPolyhedra and VTKExporter.exportInteractions
Modified MortarMat
Merge branch 'master' of github.com:yade/trunk
fixed computation of shearForce in Law2_PolyhedraGeom_PolyhedraPhys_Volumetric
added and modified examples for MortarMat
Merge branch 'master' of github.com:yade/trunk
added MatchMaker for E in Ip2_CmpMat_CpmMat_CpmPhys
Fixed a bug in pack.inSphere, related to question #292846
Merge branch 'master' of github.com:yade/trunk
VTKRecorder, added orientation for box export (question #293635)
Modification of CPM
Fixed ymport.textPolyhedra function (bug #1582775)
added x_y_z_r_attrs format to ymport.textExt
Added an example for generation of 'agglomerate' packing
Fixed Law2_Cpm default parameter to keep backward compatibility (question #294657)
Better default value from previous commit
Jerome Duriez (12):
+1 journal paper
Incorporating previous +1 paper in JCFpm doc
+ another journal paper
makeCloud doc changes with the hope to make it clearer for all users
Doc of TriaxStressController.porosity precised
Doc improvements of previous commit improved
Last doc improvement of previous commit
normalForce and shearForce convention (sustained by #2) precised in docs
fabricTensor() now ok for non-periodic simulations. revertSign attribute removed as well
getSpheres*() functions: getting rid of dynamic test, see http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg11956.html
fabricTensor(): unify the behavior regarding boundary interactions whether split=0 or 1: they are now disregarded in both cases
fabricTensor(): re introducing all kind of interactions in the loop, with the new possibility defining a cutoff. See http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg11982.html
Klaus Thoeni (23):
fix some typos and add some more details
fix Anton's previous commit (make doc was not working)
fix documentation for Note
some polishing
gts shift and scale apparently only take three float values, hence changed
Merge branch 'master' of github.com:yade/trunk
move grid specific functions in separate module and add some more doc
add some more examples, show same functionality as with chained cylinders
update doc
add Grid and pFacet references
Initial version of the PFacet implementation (contributed by Anna Effeindzourou)
Examples for creating pfacets
update tests according to new gridpfacet module
remove postLoad function as not used, this fixes as well serialization problem in --test
better handling of double contacts, get gid of function ScGem goOneWay
improved documentation
add definition for cylinder and cylinderConnection basen on gridConnection, add warning for chainedCylinder usage
examples for cylinder and cylinderConnection
example with many cylinders and 2 pFacets
QT5 is default now
correct some typos
similar to example in chained-cylinder-roots.py
add reference
Raphael Maurin (6):
HydroForceEngine: modify the turbulent fluctuations formulation and add a new DRW model The turbulent fluctuations model takes now the form of a function of HydroForceEngine and is not anymore called from a flag. In addition, an alternative DRW model has been added.
HydroForceEngine: adapt the averageProfile function for bi-disperse mixtures. Evaluate the streamwise, spanwise and wall-normal average particle velocity for the two defined types of particles.
HydroForceEngine: modify turbulent fluctuation model. Add a fluctuation along the spanwise (y) direction. Reset the fluctuation to zero when the particle is out of the flow (fix a bug) Comment a bit more the turbulentFluctuation function
HydroForceEngine, hpp file completing the last commit
Add references
add a link in the publications
bchareyre (1):
compute external work correctly in TriaxialStressController
==================================================
yade-1.20.0
Fri, Oct 9 21:20:00 2015 +0200
Anton Gladky (57):
Remove RELEASE file.
Simplify definition of build flags
Fix some warnings during compilation.
For clang use -fstack-protector instead of -fstack-protector-strong
Ignore project files of idea IDE
Refactoring of Math.hpp
Make minieigen external package mandatory.
Add -fstack-protector-strong only for gcc >=4.9
Some warning fixes.
Add ENABLE_PROFILING option