Re: [Yade-users] [Question #703836]: How desiredPorosity works?
Question #703836 on Yade changed: https://answers.launchpad.net/yade/+question/703836 Status: Answered => Open Jiannan Wang is still having a problem: Hello Robert, Thank you again for the answer, forgive my slow comprehensiveness: so what happen to the volume that are volume * (actualPorosity -desiredPorosity)? Do they have the physical properties of pore fluid only do not flow? Or something else? Thank you. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #703836]: How desiredPorosity works?
Question #703836 on Yade changed: https://answers.launchpad.net/yade/+question/703836 Status: Answered => Open Jiannan Wang is still having a problem: Thank you Robert, So, for the parts that got "corrected" (actualPorosity - desiredPorosity), are their thermal and mechanical properties replaced as particles'? In the THM process, are these portion act like solid or pore fluid? In short, am I correct to assume that the particles got manually swelled up to meet the desiredPorosity? Thank you again. Best Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #703836]: How desiredPorosity works?
New question #703836 on Yade: https://answers.launchpad.net/yade/+question/703836 Hello, So how dose desiredPorosity in the flow engine work? The description only says "Correct the cell volumes to reflect this desired porosity". Does that means even if I pack the particles loosely, I can just change the desiredPorosity into a low value and get a tight rock? It would be great if there is some sort of paper you can direct me to look up. Thanks. Best Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #696270]: Is there a way to create a model with different permeabilities
New question #696270 on Yade: https://answers.launchpad.net/yade/+question/696270 Hello, Is there a way to create layers with different permeability or permeability gradient? Thanks. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695245]: Error when running on HPC
Question #695245 on Yade changed: https://answers.launchpad.net/yade/+question/695245 Status: Open => Solved Jiannan Wang confirmed that the question is solved: Hello Robert, Just an update: they install the 20.04 on my account and now Yade and yadedaily seems to be working well. Thank you for the help. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #695245]: Error when running on HPC
Question #695245 on Yade changed: https://answers.launchpad.net/yade/+question/695245 Status: Answered => Open Jiannan Wang is still having a problem: Hello Robert, Yes, the same error dose not appear on my standard desktop. I think they installed Yade inside a ubuntu 21.04 singularity container just for me. I'll ask them for a new installation. Thank you. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #695245]: Error when running on HPC
New question #695245 on Yade: https://answers.launchpad.net/yade/+question/695245 Hello, I'm trying to run Yade on HPC. Our IT helped me set up a singularity under my account. It seems to be OK with launching Yade. But when I actually tried to run the script same as the one in the thermal coupling example [1] (omitted the graphic plot part), the following error occurred after 6000 iterations: ThreadRunner:35 void yade::ThreadRunner::run(): Exception occured: CGAL ERROR: assertion violation! Expr: dexp != 2047 File: /usr/include/CGAL/Mpzf.h Line: 448 Explanation: Creating an Mpzf from infinity or NaN. I tried to typed printAllVersions(), I got the following: ``` Yade version : 2021.01a Yade features : BoostLog PrecisionDouble Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV TWOPHASEFLOW SPH FEMLIKE GL2PS LBMFLOW THERMAL PARTIALSAT PotentialParticles Yade config dir: ~/.yade Yade precision : 53 bits, 15 decimal places, without mpmath ``` Libraries used : | library | cmake | C++ | | - | - | --- | | boost | 1.74.0| 1.74.0 | | cgal | | 5.2 | | cmake | 3.18.4| | | compiler | /usr/bin/c++ 10.2.1 | gcc 10.2.1 | | eigen | 3.3.9 | 3.3.9 | | freeglut | 2.8.1 | | | gl| | 20190805| | ipython | 7.19.0| | | metis | | 5.1.0 | | openblas | | OpenBLAS 0.3.10| | python| 3.9.1 | 3.9.1 | | qglviewer | | 2.6.3 | | qt| | 5.15.2 | | sqlite| | 3.34.0 | | suitesparse | 5.8.1 | 5.8.1 | | vtk | 9.0.1 | 9.0.1 | ``` Linux version : Ubuntu Hirsute Hippo (development branch) Architecture : amd64 Little endian : True ``` I'm wondering where it may go wrong? What is missing from the installation that cause this problem. Thank you. Best Jiannan [1]: https://gitlab.com/yade-dev/trunk/-/blob/master/examples/ThermalEngine/thermoHydroMechanical_coupling.py -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #693260]: Yade crashes at "show 3D" in Ubuntu 20.04
Question #693260 on Yade changed: https://answers.launchpad.net/yade/+question/693260 Status: Answered => Solved Jiannan Wang confirmed that the question is solved: Hello Janek, Sorry for the late response. I just update the yadedaily. It's working great. Thank you so much for the swift patch. Best Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #693260]: Yade crashes at "show 3D" in Ubuntu 20.04
Question #693260 on Yade changed: https://answers.launchpad.net/yade/+question/693260 Jiannan Wang posted a new comment: Hello Janek, Thank you so much for all these efforts. I'm very much looking forward the new update. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #693260]: Yade crashes at "show 3D" in Ubuntu 20.04
Question #693260 on Yade changed: https://answers.launchpad.net/yade/+question/693260 Jiannan Wang posted a new comment: Hello Janek, Sorry about the late reply. The crash only happens when I click the "X" bottom. Clicking the 'Show 3D' button seems fine, didn't realized that. Thank you for the nice hint! I'm not sure about what is the appropriate protocol: should I leave this thread open or close it? Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #693260]: Yade crashes at "show 3D" in Ubuntu 20.04
Question #693260 on Yade changed:
https://answers.launchpad.net/yade/+question/693260
Status: Answered => Open
Jiannan Wang is still having a problem:
Hello Janek,
Thank you so much for troubleshooting for me step by step. I used
yadedaily -f6, and there is the output:
Welcome to Yade 20201004-4238~57d1c9c~focal1
Using python version: 3.8.2 (default, Jul 16 2020, 14:00:26)
[GCC 9.3.0]
LOGGER Warning: setting "Default" log level higher than MAX_LOG_LEVEL=5 will
have no effect. Logs will not be printed, they were removed during compilation.
LOGGER Warning: to be able to use "Default"=6 you have to recompile yade with
cmake option MAX_LOG_LEVEL=6 or higher.
_log.cpp:49 void yade::setLevel(std::string, int): filter log level for
Default has been set to 6
Logging:189 void Logging::setNamedLogLevel(const string&, short int):
setting "Default" log level to 6
LOGGER Warning: setting "Default" log level higher than MAX_LOG_LEVEL=5 will
have no effect. Logs will not be printed, they were removed during compilation.
LOGGER Warning: to be able to use "Default"=6 you have to recompile yade with
cmake option MAX_LOG_LEVEL=6 or higher.
_log.cpp:49 void yade::setLevel(std::string, int): filter log level for
Default has been set to 6
TCP python prompt on localhost:9000, auth cookie `acyduk'
XMLRPC info provider on http://localhost:21000
OpenGLRenderer:84 void yade::OpenGLRenderer::initgl(): (re)initializing
GL for gldraw methods.
[[ ^L clears screen, ^U kills line. F12 controller, F11 3D view (press "h" in
3D view for help), F10 both, F9 generator, F8 plot. ]]
In [1]: yade.qt.Controller()
In [2]: GLViewer:523 void yade::GLViewer::centerScene(const Real&, const
Vector3r&, const Vector3r&, int): Select with shift, press 'm' to move.
GLViewer:535 void yade::GLViewer::centerScene(const Real&, const
Vector3r&, const Vector3r&, int): scene's bound not yet calculated or has zero
or nan dimension(s), attempt get that from bodies' positions.
GLViewer:551 void yade::GLViewer::centerScene(const Real&, const
Vector3r&, const Vector3r&, int): No min/max computed from bodies either,
setting cube (-1,-1,-1)×(1,1,1)
GLViewer:559 void yade::GLViewer::centerScene(const Real&, const
Vector3r&, const Vector3r&, int): Got scene box min=-1 -1 -1 and max=1 1 1
GLViewer:563 void yade::GLViewer::centerScene(const Real&, const
Vector3r&, const Vector3r&, int): Scene center=0 0 0, halfSize=1 1 1, radius=1,
suggestedRadius=-1
GLViewer:523 void yade::GLViewer::centerScene(const Real&, const
Vector3r&, const Vector3r&, int): Select with shift, press 'm' to move.
GLViewer:535 void yade::GLViewer::centerScene(const Real&, const
Vector3r&, const Vector3r&, int): scene's bound not yet calculated or has zero
or nan dimension(s), attempt get that from bodies' positions.
GLViewer:551 void yade::GLViewer::centerScene(const Real&, const
Vector3r&, const Vector3r&, int): No min/max computed from bodies either,
setting cube (-1,-1,-1)×(1,1,1)
GLViewer:559 void yade::GLViewer::centerScene(const Real&, const
Vector3r&, const Vector3r&, int): Got scene box min=-1 -1 -1 and max=1 1 1
GLViewer:563 void yade::GLViewer::centerScene(const Real&, const
Vector3r&, const Vector3r&, int): Scene center=0 0 0, halfSize=1 1 1, radius=1,
suggestedRadius=-1
## The following is the terminal output when I closed the 3D
view and crashed.
GLViewer:53 static void yade::GLViewer::staticCloseEvent(QCloseEvent*,
int): Accept this event: Will emit closeView for view #0
GLViewer:55 static void yade::GLViewer::staticCloseEvent(QCloseEvent*,
int): Call OpenGLManager::self->emitCloseView for view #0
OpenGLManager:76 virtual void yade::OpenGLManager::closeViewSlot(int):
Closing primary view.
OpenGLManager:78 virtual void yade::OpenGLManager::closeViewSlot(int):
The currently closed view will be destroyed later. (QWindow insists on
accessing the about to be destroyed instance)
GLViewer:59 static void yade::GLViewer::staticCloseEvent(QCloseEvent*,
int): Finished OpenGLManager::self->emitCloseView for view #0
OpenGLManager:41 virtual void yade::OpenGLManager::cleanupViewsSlot():
mutex locked, now calling: if(not viewsLater.empty()) { ... }
GLViewer:44 virtual yade::GLViewer::~GLViewer(): Closing 0
Segmentation fault (core dumped)
Let me know.
Best regards
Jiannan
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Re: [Yade-users] [Question #693260]: Yade crashes at "show 3D" in Ubuntu 20.04
Question #693260 on Yade changed: https://answers.launchpad.net/yade/+question/693260 Status: Answered => Open Jiannan Wang is still having a problem: Hello Janek, Thank you again for the interaction. I tried to use find / -iname "_GLViewer.so*" 2> /dev/null, but nothing came back from the terminal. Also, I tried reinstalling the 20.04 and fresh installing Yade and yadedaily altogether. But it still crashes when I close the 3D view. Anything else I could do? Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #693260]: Yade crashes at "show 3D" in Ubuntu 20.04
Question #693260 on Yade changed: https://answers.launchpad.net/yade/+question/693260 Status: Answered => Open Jiannan Wang is still having a problem: Hello Janek, Thank you for replying so fast. I don't know why I could have a message from 8 months old version since I only start to use Yade on this desktop (run Parallel on Mac) from mid September ... I updated yadedaily after I update to ubuntu 20.04 from 18.04. For me, the crash only occurs in 20.04. Is there anything I can do to find out where may go wrong? Thank you. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #693260]: Yade crashes at "show 3D" in Ubuntu 20.04
Question #693260 on Yade changed: https://answers.launchpad.net/yade/+question/693260 Status: Needs information => Open Jiannan Wang gave more information on the question: Hello Janek, For me, the crash only happen when I open and then close the 3D view from the controller. Otherwise the simulation itself is fine. I tried to open the controller without actual running anything. I just copy and past everything from the terminal to here just in case: Welcome to Yade 2020.01a Using python version: 3.8.2 (default, Jul 16 2020, 14:00:26) [GCC 9.3.0] LOGGER Warning: setting "Default" log level higher than MAX_LOG_LEVEL=5 will have no effect. Logs will not be printed, they were removed during compilation. LOGGER Warning: to be able to use "Default"=6 you have to recompile yade with cmake option MAX_LOG_LEVEL=6 or higher. _log.cpp:49 void yade::setLevel(std::string, int): filter log level for Default has been set to 6 Logging:187 void Logging::setNamedLogLevel(const string&, short int): setting "Default" log level to 6 LOGGER Warning: setting "Default" log level higher than MAX_LOG_LEVEL=5 will have no effect. Logs will not be printed, they were removed during compilation. LOGGER Warning: to be able to use "Default"=6 you have to recompile yade with cmake option MAX_LOG_LEVEL=6 or higher. _log.cpp:49 void yade::setLevel(std::string, int): filter log level for Default has been set to 6 TCP python prompt on localhost:9000, auth cookie `csdkyu' XMLRPC info provider on http://localhost:21000 OpenGLRenderer:68 void yade::OpenGLRenderer::initgl(): (re)initializing GL for gldraw methods. [[ ^L clears screen, ^U kills line. F12 controller, F11 3D view (press "h" in 3D view for help), F10 both, F9 generator, F8 plot. ]] In [1]: yade.qt.Controller() In [2]: GLViewer:351 void yade::GLViewer::centerScene(): Select with shift, press 'm' to move. GLViewer:360 void yade::GLViewer::centerScene(): scene's bound not yet calculated or has zero or nan dimension(s), attempt get that from bodies' positions. GLViewer:368 void yade::GLViewer::centerScene(): No min/max computed from bodies either, setting cube (-1,-1,-1)×(1,1,1) GLViewer:371 void yade::GLViewer::centerScene(): Got scene box min=-1 -1 -1 and max=1 1 1 GLViewer:375 void yade::GLViewer::centerScene(): Scene center=0 0 0, halfSize=1 1 1, radius=1 GLViewer:351 void yade::GLViewer::centerScene(): Select with shift, press 'm' to move. GLViewer:360 void yade::GLViewer::centerScene(): scene's bound not yet calculated or has zero or nan dimension(s), attempt get that from bodies' positions. GLViewer:368 void yade::GLViewer::centerScene(): No min/max computed from bodies either, setting cube (-1,-1,-1)×(1,1,1) GLViewer:371 void yade::GLViewer::centerScene(): Got scene box min=-1 -1 -1 and max=1 1 1 GLViewer:375 void yade::GLViewer::centerScene(): Scene center=0 0 0, halfSize=1 1 1, radius=1 # The crash happened when I closed the "Show 3D" window. Here is the message from the terminal: GLViewer:50 virtual void yade::GLViewer::closeEvent(QCloseEvent*): Will emit closeView for view #0 OpenGLManager:52 virtual void yade::OpenGLManager::closeViewSlot(int): Closing primary view. Segmentation fault (core dumped) ### Thank you. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #693260]: Yade crashes at "show 3D" in Ubuntu 20.04
Question #693260 on Yade changed: https://answers.launchpad.net/yade/+question/693260 Status: Answered => Open Jiannan Wang is still having a problem: Hello Janek, Thank you for replying so fast. I was using yadedaily. Here is the output of printAllVersions(): ``` Yade version : 20201002-4236~57d1c9c~focal1 Yade features : BoostLog RealHP mpmath PrecisionDouble Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV MPI TWOPHASEFLOW FEMLIKE GL2PS LBMFLOW THERMAL PotentialParticles PotentialBlocks Yade config dir: ~/.yadedaily Yade precision : 53 bits, 15 decimal places, with mpmath Yade RealHP<…> : (15, 33, 45, 60, 120, 150, 300) decimal digits in C++, (15, 33) decimal digits accessible from python ``` Libraries used : | library | cmake| C++| | - | | -- | | boost | 1.71.0 | 1.71.0 | | cgal | | 5.0.2 | | clp | 1.17.5 | 1.17.5 | | cmake | 3.16.3 || | coinutils | 2.11.4 | 2.11.4 | | compiler | /usr/bin/c++ 9.3.0 | gcc 9.3.0 | | eigen | 3.3.7| 3.3.7 | | freeglut | 2.8.1|| | gl| | 20190805 | | ipython | 7.13.0 || | metis | | 5.1.0 | | mpi | 3.1 | ompi:4.0.3 | | mpi4py| 3.0.3|| | mpmath| 1.1.0|| | openblas | | OpenBLAS 0.3.8| | python| 3.8.2| 3.8.2 | | qglviewer | | 2.6.3 | | qt| | 5.12.8 | | sphinx| 1.8.5-final-0|| | sqlite| | 3.31.1 | | suitesparse | 5.7.1| 5.7.1 | | vtk | 6.3.0| 6.3.0 | Linux version: Ubuntu 20.04.1 LTS # Thank you. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #693260]: Yade crashes at "show 3D" in Ubuntu 20.04
New question #693260 on Yade: https://answers.launchpad.net/yade/+question/693260 Hello, I updated my ubuntu to 20.04. Yade can run fine except it crashes everything I open "Show 3D" in the controller. The only message shown in the terminal is Segmentation fault (core dumped). Any idea what went wrong? Thanks. Best Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692497]: Point source for Thermal Engine?
Question #692497 on Yade changed: https://answers.launchpad.net/yade/+question/692497 Jiannan Wang posted a new comment: Hello Robert, That really helps a lot. Thank you again. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692497]: Point source for Thermal Engine?
Question #692497 on Yade changed: https://answers.launchpad.net/yade/+question/692497 Jiannan Wang posted a new comment: Hello Robert, Thank you for the update. Maybe just a side question: what is the difference between setCellTImposed and setCellTemperature? Thank you again. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
Question #692194 on Yade changed: https://answers.launchpad.net/yade/+question/692194 Status: Answered => Solved Jiannan Wang confirmed that the question is solved: Hello Robert, I think I find out where I did wrong: I set ignoreFictiousConduction=True. Though I'm not clear why exactly ... But now the script seems working fine. Thank yo again for all the helps. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692798]: thermal.tempDependentFluidBeta=False
Question #692798 on Yade changed: https://answers.launchpad.net/yade/+question/692798 Status: Answered => Solved Jiannan Wang confirmed that the question is solved: Hello Robert, Thank you for the clarification. That really answers my question. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692798]: thermal.tempDependentFluidBeta=False
Question #692798 on Yade changed: https://answers.launchpad.net/yade/+question/692798 Status: Answered => Open Jiannan Wang is still having a problem: Hello Robert, Thank you for replying so fast. Just to make sure I understand, by setting it off, the thermal expansion of fluid is nonlinear or just no thermal expansion? Thank you again. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #692798]: thermal.tempDependentFluidBeta=False
New question #692798 on Yade: https://answers.launchpad.net/yade/+question/692798 Hello, The default setting of the thermal engine is tempDependentFluidBeta=False. And it says "If true, fluid volumetric thermal expansion is temperature dependent (linear model between 20-70 degC)". I thought the fluid volumetric thermal expansion is always temperature dependent? Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
Question #692194 on Yade changed: https://answers.launchpad.net/yade/+question/692194 Jiannan Wang posted a new comment: Hello Robert, Thank you for all the helps and sharing. They are very helpful. I keep play around the script and see if I can make it work. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
Question #692194 on Yade changed: https://answers.launchpad.net/yade/+question/692194 Status: Answered => Open Jiannan Wang is still having a problem: Hello Robert, I tried with meshUpdateInterval=2, but the result is pretty much identical. Let me know. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
Question #692194 on Yade changed: https://answers.launchpad.net/yade/+question/692194 Jiannan Wang posted a new comment: Hello Robert, Absolutely. I'll get back to you as soon as I get the result. Best regards Jiannan Wang -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
Question #692194 on Yade changed: https://answers.launchpad.net/yade/+question/692194 Jiannan Wang gave more information on the question: Hello Robert, I ran the simulation as it is, the temperature went beyond the boundary value (45) at 155 s and up to 47.8035. The body temperature and the pore pressure curve looks a little bit funny. Body and water temperature in the middle looks like [1] and the pore pressure in the middle looks like [2]. Hope it is OK to attach google link here. Thank you again. Best regards Jiannan [1] https://drive.google.com/file/d/1FiV8S1L-2J4mnV9l9-NWtw6zI2gvZQhM/view?usp=sharing [2 ] https://drive.google.com/file/d/1YEaPS-lSdf5XuWVcfAAacmkF7Xoz6dMp/view?usp=sharing -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
Question #692194 on Yade changed: https://answers.launchpad.net/yade/+question/692194 Status: Needs information => Open Jiannan Wang gave more information on the question: Hello Robert, Thank you for being so patient. I used the yadedaily (20200829-4169~e627a44~bionic1) in the VritualBox on a Mac. I give 3 cores to the VirtualBox, but I didn't run it parallel. Here is the printAllVersions() output. I will re-run the exact setting again and keep you posted with more detail of how simulation ended. ``` Yade version : 20200829-4169~e627a44~bionic1 Yade features : BoostLog PrecisionDouble Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV MPI TWOPHASEFLOW FEMLIKE GL2PS LBMFLOW THERMAL PotentialParticles PotentialBlocks Yade config dir: ~/.yadedaily Yade precision : 53 bits, 15 decimal places, without mpmath ``` Libraries used : | library | cmake| C++ | | - | | --- | | boost | 106501 | 1.65.1 | | cgal | | 4.11| | clp | 1.16.11 | 1.16.11 | | cmake | 3.10.2 | | | coinutils | 2.10.14 | 2.10.14 | | compiler | /usr/bin/c++ 7.5.0 | gcc 7.5.0 | | eigen | 3.3.4| 3.3.4 | | freeglut | 2.8.1| | | gl| | 20190911| | ipython | 5.5.0| | | metis | | 5.1.0 | | mpi | 3.1 | ompi:2.1.1 | | mpi4py| 2.0.0| | | openblas | | OpenBLAS 0.2.20| | python| 3.6.9| 3.6.9 | | qglviewer | | 2.6.3 | | qt| | 5.9.5 | | sphinx| 1.6.7-final-0| | | sqlite| | 3.22.0 | | suitesparse | 5.1.2| 5.1.2 | | vtk | 6.3.0| 6.3.0 | Linux version: Ubuntu 18.04.5 LTS Best regards Jiannan Wang -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
Question #692194 on Yade changed: https://answers.launchpad.net/yade/+question/692194 Status: Solved => Open Jiannan Wang is still having a problem: Hello Robert, Just a follow-up update, I ran the code as in [1], but the temperature still went beyond thermalBndCondValue. Also, only changing the side of the boundaries (both pressure and thermal) also seems affect the result: such as changing from z-,z+ to x-, x+. I'll try to run it with smaller time step and seem what may happen (tried to increase the density scale to 1e20 and 1e30 but no luck yet). Best regards Jiannan Wang [1]https://gitlab.com/yade-dev/trunk/-/merge_requests/519 -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
Question #692194 on Yade changed: https://answers.launchpad.net/yade/+question/692194 Status: Answered => Solved Jiannan Wang confirmed that the question is solved: Hello Robert, Thank you so much for all the explanations and sharing the new example script. They are incredibly helpful. I'll work through them to have better understanding. This indeed solve the irritating puzzle I have been having. Best regards Jiannan Wang -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692497]: Point source for Thermal Engine?
Question #692497 on Yade changed: https://answers.launchpad.net/yade/+question/692497 Status: Answered => Solved Jiannan Wang confirmed that the question is solved: Hello Robert, Thank you for the help. That solves my question. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #692497]: Point source for Thermal Engine?
New question #692497 on Yade: https://answers.launchpad.net/yade/+question/692497 Hello, I'm wondering is there a way to impose point or point-ish heat source for thermal engine, something similar to the point influx in the flow engine? Thanks. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
Question #692194 on Yade changed: https://answers.launchpad.net/yade/+question/692194 Status: Answered => Open Jiannan Wang is still having a problem: Hello Robert, Thank yo for your suggestions and sorry for my delayed response. I tried to use thermal.minimumFluidCondDist = minimum particle diameter but still no luck. The only difference is the temperature curve now went smoothly as "normal" across the pre-set boundary temperature. Maybe I did something wrong? Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
Question #692194 on Yade changed: https://answers.launchpad.net/yade/+question/692194 Status: Answered => Open Jiannan Wang is still having a problem: Hello Robert, Thank you again on these series questions. I tried to reduced the time step by 1e-6 but still no luck: the temperature grown asymptomatically toward the target temperature and stayed there flat for a while. Then jumped cross the target temperature and grown at faster speed. The pore pressure didn't decrease as expected when the temperature reached the target temperature: only decrease a little bit then went up as the temperature crossed the target temperature. If I decrease the time step more, the computing time would be astronomically increase. Do you have any tip? Or did I missed something when setting up the thermal engine? Thanks. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #692194]: Body temperature rise higher than thermalBndCondValue
New question #692194 on Yade:
https://answers.launchpad.net/yade/+question/692194
Hello,
I'm trying to explore the thermal expansion with Yade, similar to the paper
[1]. But while I heated up one side of the boundary:
thermal.thermalBndCondValue=[343.15,0,0,0,0,0], the temperature of the body
went up beyond the boundary temperature. I'm wondering where did I go wrong?
Thanks. Here is the MWE:
###
from yade import pack, ymport, plot, utils, export, timing
import numpy as np
young=5e6
mn,mx=Vector3(0,0,0),Vector3(0.05,0.05,0.05)
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(30),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp=pack.SpherePack()
sp.makeCloud(mn,mx,rMean=0.0015,rRelFuzz=0.333,num=1000)
sp.toSimulation(color=(0.752, 0.752, 0.752),material='spheres')
triax=TriaxialStressController(
maxMultiplier=1.+2e4/young,
finalMaxMultiplier=1.+2e3/young,
thickness = 0,
stressMask = 7,
internalCompaction=True,
)
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=1.5,label='is2aabb'),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=1.5,label='ss2sc'),Ig2_Box_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
),
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.5),
triax,
FlowEngine(dead=1,label="flow",multithread=False),
ThermalEngine(dead=1,label='thermal'),
NewtonIntegrator(damping=0.5)
]
O.step()
ss2sc.interactionDetectionFactor=-1
is2aabb.aabbEnlargeFactor=-1
O.dt=0.1e-5
O.dynDt=False
tri_pressure = 1
triax.goal1=triax.goal2=triax.goal3=-tri_pressure
while 1:
O.run(1000, True)
unb=unbalancedForce()
print('unbalanced force:',unb,' mean stress: ',triax.meanStress)
if unb<0.01 and abs(-tri_pressure-triax.meanStress)/tri_pressure<0.001:
break
triax.internalCompaction=False
for b in O.bodies:
if isinstance(b.shape, Sphere):
b.dynamic=False
flow.dead=0
flow.defTolerance=0.003
flow.meshUpdateInterval=100
flow.boundaryUseMaxMin=[1,1,1,1,1,1]
flow.useSolver=4
flow.permeabilityFactor= 1
flow.viscosity= 0.001
flow.bndCondIsPressure=[0,0,0,0,0,0]
flow.bndCondValue=[0,0,0,0,0,0]
flow.thermalEngine=True
flow.debug=False
flow.fluidBulkModulus=2.2e11
flow.fluidRho = 997
flow.fluidCp = 4181.7
flow.bndCondIsTemperature=[0,0,0,0,0,0]
flow.thermalEngine=True
flow.thermalBndCondValue=[0,0,0,0,0,0]
flow.tZero=333.15
flow.pZero=0
thermal.dead=0
thermal.debug=False
thermal.fluidConduction=True
thermal.ignoreFictiousConduction=True
thermal.conduction=True
thermal.thermoMech=True
thermal.solidThermoMech = True
thermal.fluidThermoMech = True
thermal.advection=True
thermal.bndCondIsTemperature=[1,0,0,0,0,0]
thermal.thermalBndCondValue=[343.15,0,0,0,0,0]
thermal.fluidK = 0.6069
thermal.fluidConductionAreaFactor=1.
thermal.uniformReynolds=10
thermal.particleT0 = 333.15
thermal.particleDensity=2600.
thermal.particleK = 2.
thermal.particleCp = 710.
thermal.tsSafetyFactor=0
thermal.useKernMethod=False
thermal.useHertzMethod=True
timing.reset()
O.dt=1e-5
O.run(1,1)
def bodyByPos(x,y,z):
cBody = O.bodies[1]
cDist = Vector3(100,100,100)
for b in O.bodies:
if isinstance(b.shape, Sphere):
dist = b.state.pos - Vector3(x,y,z)
if np.linalg.norm(dist) < np.linalg.norm(cDist):
cDist = dist
cBody = b
return cBody
bodyOfInterest = bodyByPos(0.025,0.025,0.025)
from yade import plot
def history():
plot.addData(
ftemp1=flow.getPoreTemperature((0.025,0.025,0.025)),
p=flow.getPorePressure((0.025,0.025,0.025)),
t=O.time,
i = O.iter,
bodyOfIntTemp = O.bodies[bodyOfInterest.id].state.temp,
)
plot.saveDataTxt('Record.txt',vars=('t','i','p','ftemp1','bodyOfIntTemp'))
O.engines=O.engines+[PyRunner(iterPeriod=200,command='history()',label='recorder')]
plot.plots={'t':(('ftemp1','k-'),('bodyOfIntTemp','r-')), 't ':('p')} #
plot.plot(subPlots=False)
O.run()
Best regards
Jiannan
[1]: https://mercurylab.co.uk/dem8/wp-content/uploads/sites/4/2019/07/217.pdf
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Re: [Yade-users] [Question #692123]: Packing using ThermalEngine
Question #692123 on Yade changed: https://answers.launchpad.net/yade/+question/692123 Status: Answered => Solved Jiannan Wang confirmed that the question is solved: Hello Robert, Aha, I didn't even realized that. Thank you again. That's really helpful. Best regards Jiannan Wang -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692123]: Packing using ThermalEngine
Question #692123 on Yade changed: https://answers.launchpad.net/yade/+question/692123 Status: Answered => Open Jiannan Wang is still having a problem: Hello Robert, Thank you for pointing it out. I added density and thickness to the walls. It seems to be working. Just in case I fully understand, this is you meant by containing packing right? Really appreciate. Best regards Jiannan Wang -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692123]: Packing using ThermalEngine
Question #692123 on Yade changed:
https://answers.launchpad.net/yade/+question/692123
Status: Needs information => Open
Jiannan Wang gave more information on the question:
Hello Robert,
My mistake, I thought you meant just the packing MWE. Really appreciate
your patience. I attached the MWE in the follow. It is modified from
[1]. In order to make it not inconveniently long, I removed the saving
and plotting parts. The packing file is same as #3.
##
from yade import pack, ymport
from yade import timing
young=5.7e+10
poisson=0.235
density=2630
tensileStrength=1.2e+8
cohesion=3.5e+8
frictionAngle=radians(50)
O.materials.append(JCFpmMat(young=young,poisson=poisson,frictionAngle=frictionAngle,density=density,tensileStrength=tensileStrength,cohesion=cohesion,label='spheres'))
O.materials.append(JCFpmMat(young=young,poisson=poisson,frictionAngle=0,density=density,tensileStrength=tensileStrength,cohesion=cohesion,label='walls'))
walls=aabbWalls([(0,0,0),(0.05,0.05,0.05)],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp = O.bodies.append(ymport.textExt('compressedPack.spheres',
'x_y_z_r',material='spheres'))
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=1.5,label='is2aabb'),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=1.5,label='ss2sc'),Ig2_Box_Sphere_ScGeom()],
[Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1,label='interactionPhys')],
[Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=True,label='interactionLaw'),
Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
),
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.5),
FlowEngine(dead=1,label="flow",multithread=False),
ThermalEngine(dead=1,label='thermal'),
NewtonIntegrator(damping=0.5)
]
O.step()
ss2sc.interactionDetectionFactor=-1
is2aabb.aabbEnlargeFactor=-1
for b in O.bodies:
if isinstance(b.shape, Sphere):
b.dynamic=False
flow.dead=0
flow.defTolerance=-0.003
flow.meshUpdateInterval=-100
flow.boundaryUseMaxMin=[1,1,1,1,1,1]
flow.breakControlledRemesh=True
flow.useSolver=4
flow.permeabilityFactor= 1
flow.viscosity= 0.001
flow.bndCondIsPressure=[0,0,0,0,0,0]
flow.bndCondValue=[0,0,0,0,0,0]
flow.thermalEngine=True
flow.debug=False
flow.fluidRho = 997
flow.fluidCp = 4181.7
flow.bndCondIsTemperature=[1,0,0,0,0,0]
flow.thermalEngine=True
flow.thermalBndCondValue=[343.15,0,0,0,0,0]
flow.tZero=333.15
flow.pZero=0
thermal.dead=0
thermal.debug=False
thermal.fluidConduction=True
thermal.ignoreFictiousConduction=True
thermal.conduction=True
thermal.thermoMech=True
thermal.solidThermoMech = True
thermal.fluidThermoMech = True
thermal.advection=True
thermal.bndCondIsTemperature=[1,0,0,0,0,0]
thermal.thermalBndCondValue=[343.15,0,0,0,0,0]
thermal.fluidK = 0.6069
thermal.fluidConductionAreaFactor=1.
thermal.uniformReynolds=10
thermal.particleT0 = 333.15
thermal.particleDensity=2600.
thermal.particleK = 2.
thermal.particleCp = 710.
thermal.tsSafetyFactor=0
thermal.useKernMethod=True
thermal.useHertzMethod=False
timing.reset()
O.dt=1e-12
O.dynDt=False
O.run(1,1)
#
Thank yo again.
Best regards
Jiannan
[1]: https://gitlab.com/yade-
dev/trunk/-/blob/master/examples/ThermalEngine/noFlowScenario.py
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Re: [Yade-users] [Question #692123]: Packing using ThermalEngine
Question #692123 on Yade changed:
https://answers.launchpad.net/yade/+question/692123
Status: Needs information => Open
Jiannan Wang gave more information on the question:
Hello Robert,
Sorry for the mistake. I put the scene back to the MWE, the result is
still the same:
from yade import export
young=1e9
tt=TriaxialTest(StabilityCriterion=.001,
compactionFrictionDeg=radians(3),internalCompaction=True,
radiusMean=0.004,numberOfGrains=1000,
upperCorner=(0.05,0.05,0.05),lowerCorner=(0,0,0),thickness=0.01,radiusStdDev=0.3,sigmaIsoCompaction=-1,maxMultiplier=1.+2e4/young,finalMaxMultiplier=1.+2e3/young)
tt.generate("CubicPack.yade")
O.load('CubicPack.yade')
O.run(2,1)
export.text('CubicPack.spheres')
Also I tried the one similar to [1], still no luck. Here is the modified
MWE just in case:
#
from yade import pack, export
stabilityThreshold=0.01
young=1e9
mn,mx=Vector3(0,0,0),Vector3(0.05,0.05,0.05)
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(3),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp=pack.SpherePack()
sp.makeCloud(mn,mx,rMean=0.004,rRelFuzz=0.0,num=1000)
sp.toSimulation(material='spheres')
triax=TriaxialStressController(
maxMultiplier=1.+2e4/young,
finalMaxMultiplier=1.+2e3/young,
thickness = 0,
stressMask = 7,
internalCompaction=True,
)
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom_FrictPhys_CundallStrack()]
),
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
triax,
NewtonIntegrator(damping=0.5)
]
O.dt=0.1e-5
O.dynDt=False
tri_pressure = 1
triax.goal1=triax.goal2=triax.goal3=-tri_pressure
while 1:
O.run(1000, True)
unb=unbalancedForce()
print('unbalanced force:',unb,' mean stress: ',triax.meanStress)
if unbhttps://gitlab.com/yade-dev/trunk/-/blob/master/examples/triax-tutorial/script-session1.py
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[Yade-users] [Question #692123]: Packing using ThermalEngine
New question #692123 on Yade:
https://answers.launchpad.net/yade/+question/692123
Hello,
This is more like extended following up question of [1]. I'm trying to explore
thermal expansion by modifying example [2]:
Active the ThermoMech in section [4], and heat up one of the boundaries (adding
temperature to one of the thermal boundary conditions in [5]). It seems to work
using the packing file in the example ([3]) at dt = 1e-12, or start with dt =
1e-12 for few iterations, i.e. 500 iterations, and then switch back to 1e-9.
But it is not working with my own generated packing. I try to keep the
dimensions and the partial size as same as the one in the example ([3]). No
matter how small the dt is (even 1e-20), the partials inside the cubic
immediately disappear. Is there something I missed on the packing side? Or I
messed up on some other fronts as while? I attach a MEW packing script:
from yade import export
young=1e9
tt=TriaxialTest(StabilityCriterion=.001,
compactionFrictionDeg=radians(3),internalCompaction=True,
radiusMean=-0.004,numberOfGrains=1000,
upperCorner=(0.05,0.05,0.05),lowerCorner=(0,0,0),thickness=0.01,radiusStdDev=0.3,sigmaIsoCompaction=-1,maxMultiplier=1.+2e4/young,finalMaxMultiplier=1.+2e3/young)
O.run(2,1)
export.text('CubicPack.spheres')
Thanks in advance.
Best regards
Jiannan
[1]: https://answers.launchpad.net/yade/+question/692076
[2]:
https://gitlab.com/yade-dev/trunk/-/blob/master/examples/ThermalEngine/noFlowScenario.py
[3]:
https://gitlab.com/yade-dev/trunk/-/blob/master/examples/ThermalEngine/5cmEdge_1mm.spheres
[4]:
https://gitlab.com/yade-dev/trunk/-/blob/master/examples/ThermalEngine/noFlowScenario.py#L125-127
[5]:
https://gitlab.com/yade-dev/trunk/-/blob/master/examples/ThermalEngine/noFlowScenario.py#L129-130
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Re: [Yade-users] [Question #692076]: b.dynamic=False in ThermalEngine example
Question #692076 on Yade changed: https://answers.launchpad.net/yade/+question/692076 Status: Answered => Solved Jiannan Wang confirmed that the question is solved: Hello Robert, Thank you for willing to help, I'll open another thread. Best regards Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #692076]: b.dynamic=False in ThermalEngine example
Question #692076 on Yade changed:
https://answers.launchpad.net/yade/+question/692076
Status: Answered => Open
Jiannan Wang is still having a problem:
Hello Robert,
Thank you for the help. I decrease the time step down to 1e-12, and it
is finally working. If I use dt = 1e-12 for few iterations, i.e. 500
iterations, and then switch back to 1e-9, seems also OK.
But all this only work on the exact pack file in the example (sphere file in
[1]). I try to create my own pack, with roughly the same dimension and
parasitical radius, still cannot get it works (even with dt = 1e-30 ...). Is
there something I missed on the packing side? I attach a MEW packing script:
from yade import export
young=1e9
tt=TriaxialTest(StabilityCriterion=.001,
compactionFrictionDeg=radians(3),internalCompaction=True,
radiusMean=-0.004,numberOfGrains=1000,
upperCorner=(0.05,0.05,0.05),lowerCorner=(0,0,0),thickness=0.01,radiusStdDev=0.3,sigmaIsoCompaction=-1,maxMultiplier=1.+2e4/young,finalMaxMultiplier=1.+2e3/young)
O.run(2,1)
export.text('CubicPack.spheres')
3
Best regards
Jiannan Wang
[1]: https://gitlab.com/yade-
dev/trunk/-/blob/master/examples/ThermalEngine/5cmEdge_1mm.spheres
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Re: [Yade-users] [Question #692076]: b.dynamic=False in ThermalEngine example
Question #692076 on Yade changed: https://answers.launchpad.net/yade/+question/692076 Status: Answered => Open Jiannan Wang is still having a problem: Hello Robert, Yeah ... The spheres immediately disappear, even for the nonflowScenario [1] and thermoMech=False. Also, in nonflowScenario [1], if I heat up one of the wall and set b.dynamic=False and fluidThermoMech=True, all the spheres, except the ones on the heated wall, disappear. Where did I mess up? Best regards Jiannan Wangg [1]:https://gitlab.com/yade- dev/trunk/-/blob/master/examples/ThermalEngine/noFlowScenario.py -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #692076]: b.dynamic=False in ThermalEngine example
New question #692076 on Yade: https://answers.launchpad.net/yade/+question/692076 Hello, I'm trying to learn through the thermal engine example in [1]. If I remove the b.dynamic=False: comments the section of [2], the temperature won't change (the temperature plot just becomes flat lines). What is the reason behind this? The reason I'm asking is that I want to explore the thermal expansion effect on the strain changes of the body. Setting b.dynamic=False seems counterintuitive? Any tip? Thanks! Best regards Jiannan [1]: https://gitlab.com/yade-dev/trunk/-/blob/master/examples/ThermalEngine/flowScenario.py [2]: https://gitlab.com/yade-dev/trunk/-/blob/master/examples/ThermalEngine/flowScenario.py#L100-102 -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #691115]: Question about the "0.05" in (O.bodies[i.id2].state.jointNormal1.cross(nRef)).norm()>0.05)
Question #691115 on Yade changed: https://answers.launchpad.net/yade/+question/691115 Status: Answered => Solved Jiannan Wang confirmed that the question is solved: Hello Jerome, Thank you so much for the helps. Now I can carry on my happy reading :p Best Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #691115]: Question about the "0.05" in (O.bodies[i.id2].state.jointNormal1.cross(nRef)).norm()>0.05)
Question #691115 on Yade changed: https://answers.launchpad.net/yade/+question/691115 Status: Answered => Open Jiannan Wang is still having a problem: Hello Jerome and Bruno, Thank you very much for the explanations. That really helps me understand a lot. Just a follow up question in case I'm not fully grasp the full scope of this, if that is OK: In the case of [1], while it find out the sphere is on the joint with 3 facets already, why not reorient the normal with the fourth facet as before? It is because there is not such thing as state.jointNormal4 or there are more to it? I hope it is OK to follow up in the same thread. Thank you. Best Jiannan [1]. https://gitlab.com/yade-dev/trunk/-/blob/master/examples/jointedCohesiveFrictionalPM/identifBis.py#L67-69 -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #691115]: Question about the "0.05" in (O.bodies[i.id2].state.jointNormal1.cross(nRef)).norm()>0.05)
Question #691115 on Yade changed: https://answers.launchpad.net/yade/+question/691115 Status: Answered => Open Jiannan Wang is still having a problem: Hello Bruno, Thank you for that. There is the github link: https://gitlab.com/yade- dev/trunk/-/blob/master/examples/jointedCohesiveFrictionalPM/identifBis.py#L53 Best Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #691115]: Question about the "0.05" in (O.bodies[i.id2].state.jointNormal1.cross(nRef)).norm()>0.05)
New question #691115 on Yade: https://answers.launchpad.net/yade/+question/691115 Hello, I'm quit a newbie of Yade. As I am reading through the /examples/jointedCohesiveFrictionalPM/, there is this if condition in [1] that is puzzling to me: where is the number 0.05 came from? What is the reason of choosing this particular number? Thanks. Best Jiannan [1]. https://github.com/yade/trunk/blob/master/examples/jointedCohesiveFrictionalPM/identifBis.py#L53 -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690820]: VTKRecorder: Aborted (core dumped)
Question #690820 on Yade changed: https://answers.launchpad.net/yade/+question/690820 Jiannan Wang posted a new comment: Hello Robert, Thank you for the advice. Probably not the space and write privilege issue since I tested the MWE on ~/Desktop. Here is the output of ls -ld and df -h: ## drwxr-xr-x 13 odisi odisi 12288 May 22 11:35 /home/odisi/Desktop # odisi@odisi-linux-1:~/Desktop$ df -h Filesystem Size Used Avail Use% Mounted on udev 16G 0 16G 0% /dev tmpfs 3.2G 2.3M 3.2G 1% /run /dev/nvme0n1p3 463G 132G 309G 30% / tmpfs16G 146M 16G 1% /dev/shm tmpfs 5.0M 4.0K 5.0M 1% /run/lock tmpfs16G 0 16G 0% /sys/fs/cgroup /dev/loop1 141M 141M 0 100% /snap/gnome-3-26-1604/92 /dev/loop3 141M 141M 0 100% /snap/gnome-3-26-1604/98 /dev/loop2 157M 157M 0 100% /snap/gnome-3-28-1804/110 /dev/loop4 2.3M 2.3M 0 100% /snap/gnome-system-monitor/145 /dev/loop5 94M 94M 0 100% /snap/core/8935 /dev/loop6 63M 63M 0 100% /snap/gtk-common-themes/1506 /dev/loop8 7.9M 7.9M 0 100% /snap/evince/391 /dev/loop7 94M 94M 0 100% /snap/core/9066 /dev/loop9 3.8M 3.8M 0 100% /snap/gnome-system-monitor/135 /dev/loop13 243M 243M 0 100% /snap/gnome-3-34-1804/27 /dev/loop12 7.9M 7.9M 0 100% /snap/evince/290 /dev/loop11 1.0M 1.0M 0 100% /snap/gnome-logs/93 /dev/loop10 55M 55M 0 100% /snap/gtk-common-themes/1502 /dev/loop14 384K 384K 0 100% /snap/gnome-characters/539 /dev/loop17 55M 55M 0 100% /snap/core18/1754 /dev/loop15 256M 256M 0 100% /snap/gnome-3-34-1804/33 /dev/nvme0n1p1 776M 53M 724M 7% /boot/efi /dev/loop18 2.5M 2.5M 0 100% /snap/gnome-calculator/748 /dev/loop19 15M 15M 0 100% /snap/gnome-characters/495 /dev/loop20 161M 161M 0 100% /snap/gnome-3-28-1804/116 /dev/loop21 1.0M 1.0M 0 100% /snap/gnome-logs/100 /dev/loop22 55M 55M 0 100% /snap/core18/1705 /dev/loop23 2.5M 2.5M 0 100% /snap/gnome-calculator/730 tmpfs 3.2G 16K 3.2G 1% /run/user/120 tmpfs 3.2G 36K 3.2G 1% /run/user/1001 ### -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690820]: VTKRecorder: Aborted (core dumped)
Question #690820 on Yade changed: https://answers.launchpad.net/yade/+question/690820 Status: Open => Solved Jiannan Wang confirmed that the question is solved: Hello Janek, Thank you for the help. I don't recall doing experiment inside VTK, maybe I did but was aware of? Do you think reinstall would help? Anyway, I'll mark this question as solved since it appears be my own problem. Thank you guys again. Best Jiannan Wang -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690820]: VTKRecorder: Aborted (core dumped)
Question #690820 on Yade changed: https://answers.launchpad.net/yade/+question/690820 Status: Needs information => Open Jiannan Wang gave more information on the question: Hello Janek, Thank you for willing to help. Here is the output. Let me know if there is anything I should provide. Best Jiannan Wang ## Yade version : 20200518-3844~fb69be8~bionic1 Yade features : BoostLog PrecisionDouble Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV MPI TWOPHASEFLOW FEMLIKE GL2PS LBMFLOW THERMAL PotentialParticles PotentialBlocks Yade config dir: ~/.yadedaily Yade precision : 64 bits, 15 decimal places, without mpmath ``` Libraries used : | library | cmake| C++ | | - | | --- | | boost | 106501 | 1.65.1 | | cgal | | 4.11| | clp | 1.16.11 | 1.16.11 | | cmake | 3.10.2 | | | coinutils | 2.10.14 | 2.10.14 | | compiler | /usr/bin/c++ 7.5.0 | gcc 7.5.0 | | eigen | 3.3.4| 3.3.4 | | freeglut | 2.8.1| | | gl| | 20190611| | ipython | 5.5.0| | | metis | | 5.1.0 | | mpi | 3.1 | ompi:2.1.1 | | mpi4py| 2.0.0| | | openblas | | OpenBLAS 0.2.20| | python| 3.6.9| 3.6.9 | | qglviewer | | 2.6.3 | | qt| | 5.9.5 | | sphinx| 1.6.7-final-0| | | sqlite| | 3.22.0 | | suitesparse | 5.1.2| 5.1.2 | | vtk | 6.3.0| 6.3.0 | Linux version: Ubuntu 18.04.4 LTS # -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690820]: VTKRecorder: Aborted (core dumped)
Question #690820 on Yade changed: https://answers.launchpad.net/yade/+question/690820 Status: Needs information => Open Jiannan Wang gave more information on the question: Hello Robert, That's very odd. Once I start, the error shows up immediately. Should I provide more system information or is there anyway I can check I may be missing beside the script itself? Thank you again. Best Jiannan Wang -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690820]: VTKRecorder: Aborted (core dumped)
Question #690820 on Yade changed: https://answers.launchpad.net/yade/+question/690820 Status: Needs information => Open Jiannan Wang gave more information on the question: Hello Robert, Oops... Sorry about the missing variable, again. The following MWE runs as expected. Thank you. Best Jiannan Wang ##3 from builtins import range from yade import pack,utils import math from pylab import rand O.materials.append(JCFpmMat(type=1,density=2500,young=1800,poisson=0.1,frictionAngle=radians(7),tensileStrength=100,cohesion=1000,label='mat')) mn,mx=Vector3(0,0,0),Vector3(1,2,1) walls=aabbWalls([mn,mx],thickness=0,material='mat') wallIds=O.bodies.append(walls) sps=pack.SpherePack() sp=pack.randomDensePack(pack.inAlignedBox(mn,mx),spheresInCell=2000,radius=1/20,returnSpherePack=True) sp.toSimulation(material='mat') O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=1)]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=1)], [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1)], [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=True,label='interactionLaw', recordCracks=True, recordMoments=True,Key='identifier',momentRadiusFactor=5,neverErase=True),Law2_ScGeom_FrictPhys_CundallStrack()] ), GlobalStiffnessTimeStepper(active=1,timestepSafetyCoefficient=0.5), NewtonIntegrator(damping=0.1), ] from yade import qt v=qt.View() O.engines=O.engines+[VTKRecorder(Key='identifier',label='vtk',iterPeriod=100,initRun=True,fileName='output-',recorders=['moments','spheres','intr','stress','velocity','bstresses','jcfpm', 'cracks'])] ## -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690820]: VTKRecorder: Aborted (core dumped)
Question #690820 on Yade changed: https://answers.launchpad.net/yade/+question/690820 Status: Needs information => Open Jiannan Wang gave more information on the question: Hello Robert, I'm sorry about the missing lines. I just added them back. It should be fine this time. Thank you again for the helps. I think I know where it gave me the error, but I don't know why Only when I add: from yade import qt v=qt.View() Things went wrong. Otherwise it works OK. Seems qt.View() and VTKRecorder cannot co-exist... Could you give me some advise? Best Jiannan Wang # from builtins import range from yade import pack,utils import math from pylab import rand O.materials.append(JCFpmMat(type=1,density=2500,young=1800,poisson=0.1,frictionAngle=radians(7),tensileStrength=100,cohesion=1000,label='mat')) mn,mx=Vector3(0,0,0),Vector3(1,2,1) walls=aabbWalls([mn,mx],thickness=0,material='mat') wallIds=O.bodies.append(walls) sps=pack.SpherePack() sp=pack.randomDensePack(pack.inAlignedBox(mn,mx),spheresInCell=2000,radius=1/20,returnSpherePack=True) sp.toSimulation(material='mat') O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intR)], [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1)], [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=True,label='interactionLaw', recordCracks=True, recordMoments=True,Key='identifier',momentRadiusFactor=5,neverErase=True),Law2_ScGeom_FrictPhys_CundallStrack()] ), GlobalStiffnessTimeStepper(active=1,timestepSafetyCoefficient=0.5), NewtonIntegrator(damping=0.1), ] from yade import qt v=qt.View() O.engines=O.engines+[VTKRecorder(Key='identifier',label='vtk',iterPeriod=iterper,initRun=True,fileName='output-',recorders=['moments','spheres','intr','stress','velocity','bstresses','jcfpm', 'cracks'])] ## -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690820]: VTKRecorder: Aborted (core dumped)
Question #690820 on Yade changed: https://answers.launchpad.net/yade/+question/690820 Status: Needs information => Open Jiannan Wang gave more information on the question: Hello Robert, Absolutely. Here is my MWE. Thanks. Best Jiannan Wang # from builtins import range from yade import pack,utils import math O.materials.append(JCFpmMat(type=1,density=2500,young=1800,poisson=0.1,frictionAngle=radians(7),tensileStrength=100,cohesion=1000,label='mat')) mn,mx=Vector3(0,0,0),Vector3(1,2,1) walls=aabbWalls([mn,mx],thickness=0,material='mat') wallIds=O.bodies.append(walls) sps=SpherePack() sp=pack.randomDensePack(pack.inAlignedBox(mn,mx),spheresInCell=2000,radius=1/20.,returnSpherePack=True) O.bodies.append([sphere(s[0],s[1],color=(0.6+0.15*rand(),0.5+0.15*rand(),0.15+0.15*rand()),material='mat1') for s in sp]) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intR)], [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1)], [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=True,label='interactionLaw', recordCracks=True, recordMoments=True,Key='identifier',momentRadiusFactor=5,neverErase=True),Law2_ScGeom_FrictPhys_CundallStrack()] ), GlobalStiffnessTimeStepper(active=1,timestepSafetyCoefficient=0.5), NewtonIntegrator(damping=0.1), ] O.engines=O.engines+[VTKRecorder(Key='identifier',label='vtk',iterPeriod=iterper,initRun=True,fileName='output-',recorders=['moments','spheres','intr','stress','velocity','bstresses','jcfpm', 'cracks'])] ## -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690820]: VTKRecorder: Aborted (core dumped)
Question #690820 on Yade changed: https://answers.launchpad.net/yade/+question/690820 Status: Needs information => Open Jiannan Wang gave more information on the question: Hello Robert, Thank you for the swift response. Sorry about the confusion: when I use DFNFlowEngine, I just run the compiled source version (as you suggest in anther thread [1]). Then I switch DFNFlowEngine to FlowEngine and run with both the compiled source version and the yadedaily. The script that I use to reproduce the error with yadedaily is just replace DFNFlowEngine with FlowEngine, everything else is the same. Also, I also tried removing the FlowEngine/DFNFlowEngine (no fluid at all). I also got the same error. [1]https://answers.launchpad.net/yade/+question/689755 -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #690820]: VTKRecorder: Aborted (core dumped)
New question #690820 on Yade: https://answers.launchpad.net/yade/+question/690820 Hello, I'm trying to inject water into aJCFpm. It is working fine until I enable the VTKRecorder, I got the following error: python3.6: /build/vtk6-VHOYAG/vtk6-6.3.0+dfsg1/IO/XML/vtkXMLOffsetsManager.h:142: void OffsetsManagerGroup::Allocate(int, int): Assertion `numElements > 0' failed. Aborted (core dumped) My Yade version: try both compiled from the source and yadedaily, same error Linux version: Ubuntu 18.04.4 LTS Did I miss anything? Thanks. Best Jiannan Here is the script: # from builtins import range from yade import pack,plot,utils import math intR=0.1 DENS=2500 YOUNG=1800 FRICT=7 ALPHA=0.1 TENS=100 COH=1000 iterper=100 O.materials.append(JCFpmMat(type=1,density=DENS,young=YOUNG,poisson=ALPHA,frictionAngle=radians(FRICT),tensileStrength=TENS,cohesion=COH,label='mat1')) mn,mx=Vector3(0,0,0),Vector3(1,2,1) # corners of the initial packing walls=aabbWalls([mn,mx],thickness=0,material='mat1') wallIds=O.bodies.append(walls) sps=SpherePack() sp=pack.randomDensePack(pack.inAlignedBox(mn,mx),spheresInCell=2000,radius=1/20.,returnSpherePack=True) O.bodies.append([sphere(s[0],s[1],color=(0.6+0.15*rand(),0.5+0.15*rand(),0.15+0.15*rand()),material='mat1') for s in sp]) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intR)], [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1)], [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=True,label='interactionLaw', recordCracks=True, recordMoments=True,Key='identifier',momentRadiusFactor=5,neverErase=True),Law2_ScGeom_FrictPhys_CundallStrack()] ), DFNFlowEngine(dead=1,label="flow"), GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.5, defaultDt=utils.PWaveTimeStep()), NewtonIntegrator(damping=0.1), ] flow.dead=0 flow.defTolerance=0.3 flow.meshUpdateInterval=1 flow.updateTriangulation=True flow.breakControlledRemesh=True flow.imposePressure(Vector3(0.5,1,0),3000) O.dt=0.1e-5 O.dynDt=False O.engines=O.engines+[VTKRecorder(Key='identifier',label='vtk',iterPeriod=iterper,initRun=True,fileName='output-',recorders=['moments','spheres','intr','stress','velocity','bstresses','jcfpm', 'cracks'])] ## -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690716]: negative volume for an ordinary pore, stack smashing detected
Question #690716 on Yade changed: https://answers.launchpad.net/yade/+question/690716 Status: Open => Solved Jiannan Wang confirmed that the question is solved: Hello Robert, I compiled the DFNFlow as you suggested and it works fine. I changed the packing and somehow it works (though I still not sure where I did wrong). Thank you for your help. -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690716]: negative volume for an ordinary pore, stack smashing detected
Question #690716 on Yade changed: https://answers.launchpad.net/yade/+question/690716 Status: Needs information => Open Jiannan Wang gave more information on the question: Hello Robert, Sorry about the missing information. Hope these are making it clearer: 1. Yade is compiled from the source[1] (not sure there is a version number) 2. Linux version: Ubuntu 18.04.4 LTS 3. The "'parallellepiped_10_persistentPlane30Deg.spheres" file is the same as shown in example in /examples/jointedCohesiveFrictionalPM: (1) running [2] with mesh file [3], then (2) running [4] with the file generted from (1) and the .stl file [5]. Thank you again. Let me know if there is anything more I should provide. Best Jiannan [1]:https://gitlab.com/yade-dev/trunk [2]:https://gitlab.com/yade-dev/trunk/-/blob/master/examples/jointedCohesiveFrictionalPM/packInGtsSurface.py [3]:https://gitlab.com/yade-dev/trunk/-/blob/master/examples/jointedCohesiveFrictionalPM/parallellepiped.gts [4]:https://gitlab.com/yade-dev/trunk/-/blob/master/examples/jointedCohesiveFrictionalPM/identificationSpheresOnJoint.py [5]: https://gitlab.com/yade-dev/trunk/-/blob/master/examples/jointedCohesiveFrictionalPM/persistentPlane30Deg.stl -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690716]: negative volume for an ordinary pore, stack smashing detected
Question #690716 on Yade changed: https://answers.launchpad.net/yade/+question/690716 Jiannan Wang gave more information on the question: Hello Robert, I have tried out the DFNFlowEngine (just swapped from FlowEngine to DFNFlowEngine), but a different type of error is showing up: negative volume for an ordinary pore (temp warning, should still be safe) negative volume for an ordinary pore (temp warning, should still be safe) negative volume for an ordinary pore (temp warning, should still be safe) negative volume for an ordinary pore (temp warning, should still be safe) Segmentation fault (core dumped) Any tip where I may be doing wrong? Thanks Jiannan -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #690716]: negative volume for an ordinary pore, stack smashing detected
Question #690716 on Yade changed: https://answers.launchpad.net/yade/+question/690716 Status: Answered => Open Jiannan Wang is still having a problem: Hello Robert, Thank you for the tips, that explains a lot. I will try out the DFNFlowEngine. One follow up question: I complied the DFNFlowEngeine as you suggested in [1]. Seems the newly complied version only works in the installed directory (in my case is ~/myYade/build/bins). So, to run the script with DFNFlowEngine, do I have to run them in the installed folder by ./yade-Unknown myScript.py? Is there a way I can make this version as default so I can run it from any other place? Thnks. Jiannan [1]https://answers.launchpad.net/yade/+question/689755 -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #690716]: negative volume for an ordinary pore, stack smashing detected
New question #690716 on Yade:
https://answers.launchpad.net/yade/+question/690716
Hello,
I'm trying to duplicate the hydraulic fracturing process in Papachristos et
al., 2017[1]. As a very newbie of Yade, I just start from the existing example.
The fractured rock is modified from example/jointedCohesiveFrictionalPM: remove
the gravity engine. Then I put a point Flux on the fracture plane (actually I'm
not quite sure it is the right way to model the hydraulic fracture). However,
when I use the FlowEngine, it gives me the following error:
negative volume for an ordinary pore (temp warning, should still be safe)
negative volume for an ordinary pore (temp warning, should still be safe)
negative volume for an ordinary pore (temp warning, should still be safe)
negative volume for an ordinary pore (temp warning, should still be safe)
negative volume for an ordinary pore (temp warning, should still be safe)
negative volume for an ordinary pore (temp warning, should still be safe)
negative volume for an ordinary pore (temp warning, should still be safe)
*** stack smashing detected ***: terminated
Aborted (core dumped)
I searched around the forum, even though there were similar questions posted
before, but I have no luck finding a effective solution for me. Here is the
script (the parallellepiped_10_persistentPlane30Deg and jointDip30_jointFrict20
files are same as example/jointedCohesiveFrictionalPM):
==
from __future__ import print_function
O=Omega()
from yade import plot, pack,utils,ymport
controling parameters
packing='parallellepiped_10_persistentPlane30Deg'
smoothContact=True
jointFrict=radians(20)
jointDil=radians(0)
output='jointDip30_jointFrict20'
maxIter=1
Import of the sphere assembly
def sphereMat(): return
JCFpmMat(type=1,young=1e8,frictionAngle=radians(30),density=3000,poisson=0.3,tensileStrength=1e6,cohesion=1e6,jointNormalStiffness=1e7,jointShearStiffness=1e7,jointCohesion=1e6,jointFrictionAngle=jointFrict,jointDilationAngle=jointDil)
print("\n In case of errors please look at README about generating
parallellepiped_10_persistentPlane30Deg.spheres file\n")
O.bodies.append(ymport.text(packing+'.spheres',scale=1.,shift=Vector3(0,0,0),material=sphereMat))
## preprocessing to get dimensions of the packing
dim=utils.aabbExtrema()
dim=utils.aabbExtrema()
xinf=dim[0][0]
xsup=dim[1][0]
X=xsup-xinf
yinf=dim[0][1]
ysup=dim[1][1]
Y=ysup-yinf
zinf=dim[0][2]
zsup=dim[1][2]
Z=zsup-zinf
## preprocessing to get spheres dimensions
R=0
Rmax=0
numSpheres=0.
for o in O.bodies:
if isinstance(o.shape,Sphere):
numSpheres+=1
R+=o.shape.radius
if o.shape.radius>Rmax:
Rmax=o.shape.radius
Rmean=R/numSpheres
inFile=open(packing+'_jointedPM.spheres','r')
for line in inFile:
if '#' in line : continue
id = int(line.split()[0])
onJ = int(line.split()[1])
nj = int(line.split()[2])
j11 = float(line.split()[3])
j12 = float(line.split()[4])
j13 = float(line.split()[5])
j21 = float(line.split()[6])
j22 = float(line.split()[7])
j23 = float(line.split()[8])
j31 = float(line.split()[9])
j32 = float(line.split()[10])
j33 = float(line.split()[11])
O.bodies[id].state.onJoint=onJ
O.bodies[id].state.joint=nj
O.bodies[id].state.jointNormal1=(j11,j12,j13)
O.bodies[id].state.jointNormal2=(j21,j22,j23)
O.bodies[id].state.jointNormal3=(j31,j32,j33)
inFile.close
joint strength degradation
for i in O.interactions:
if i.phys.isOnJoint :
if i.phys.isCohesive:
i.phys.isCohesive=False
i.phys.FnMax=0.
i.phys.FsMax=0.
newton=NewtonIntegrator(damping=0.2)
interactionRadius=1.
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=interactionRadius,label='is2aabb'),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=interactionRadius,label='ss2d3dg'),Ig2_Box_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys(),Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1,label='interactionPhys')],
[Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=smoothContact,label='interactionLaw'),Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
),
FlowEngine(dead=1,label="flow"),
GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.8),
newton,
]
from yade import qt
v=qt.Controller()
v=qt.View()
flow.dead=0
flow.defTolerance=0.3
flow.meshUpdateInterval=200
flow.useSolver=3
flow.permeabilityFactor=1
flow.viscosity=1
flow.boundaryUseMaxMin=[1,1,1,1,1,1]
flow.fluidBulkModulus=2.2e9
flow.fluidRho=1000
O.dt=0.1e-4
O.dynDt=False
flow.updateTriangulation=True
flow.bndCondIsPressure=[1,1,1,1,1,1]
flow.bndCondValue=[0,0,0,0,0,0]
flow.imposeFlux=[(0,1,0),8.3e-5]
O.run(1
