Re: [Yade-users] [Question #699072]: About the examples/ThermalEngine
Question #699072 on Yade changed: https://answers.launchpad.net/yade/+question/699072 Ziyu Wang gave more information on the question: Hello Robert! I have the latest findings, which may help solve this problem: I follow your suggestion and consider changing O.dt and the number of spheres respectively.I found something interesting.. 1.I have tried the number of spheres as 100,200,300,500,1000,2000,and the O.dt as 1e-4 to 1e-6 (I also tried using the O.dt=PWaveTimeStep(), not sure if it's appropriate).The success of the simulation does not seem to have much to do with O.dt but O.dt affects the speed of the simulation(The premise is that the simulation is successful, that is, there is temperature instead of Nan) 2.As described in 1, I found that when the number of spheres is 100,200,1000,2000, the simulation is successful (i.e. the pore and body have their own temperature rather than Nan).But 300,500,the problem still exists,like the original script (unchanged).With these scripts,there is a same warning: CHOLMOD warning: matrix not positive definite. file: ../Supernodal/t_cholmod_super_numeric.c line: 911 (Maybe this is the reason of problem?) 3.As mentioned in 2, even in the successful cases, the curves are different.In the example script, I guess the ideal curve should be to keep the pore temperature at 343.15 and gradually increase the particle temperature from 333.15 to 343.15.If I'm right, this is true only when num = 100, and in other cases, the body temperature will increase to 353.15.. What is wrong with the problem? Best regards. -- 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 #699070]: Effect of particle size on noise in the results
Question #699070 on Yade changed: https://answers.launchpad.net/yade/+question/699070 Status: Needs information => Open SO TA gave more information on the question: Hi Jan, Sorry for my not well-defined questions! I'll response to each section under your comments. > I am new to DEM and I have very little experience with YADE and DEM welcome :-) Thanks please read [1] and provide (much) more information, ideally also a MWE if possible. > I am simulating ... a bucket ... a stockpile ... please note that the simulation is not done using Yade. It is in Algoryx. As I mentioned in my first question, my question is of more DEM nature rather than a YADE one. I added image1 to provide you with an idea of what are bucket and stockpile. Image 1: https://www.dropbox.com/s/35f2vwb5vcqh9wn/Image.png?dl=0 What is "a bucket" and "a stockpile"? explained in the image (above link) What shape do they have? explained in the image (above link) What are they composed from (spheres, facets, ...)? the particles are spheres with uniform PSD. bucket is a rigid solid body. What is their mutual sizes and mutual sizes of the components? the size of the bucket and stockpile is explained in the image (above link). four particle samples of 100mm, 200mm, 300mm and 400mm are simulated. Are the components regular or not? not sure what does this mean? ... ? ... ? > when I use large particle sizes What is "large", large with respect to what? 300-400mm alone is useless information... large with respect to the size and capacity of the excavator > the results are noisy What is "the result"? Positions, velocities, energies? Numerical result or visual state? ... ? Numerical results including cycle time (the time takes the bucket to go through the granular material) and payload (the amount of the particles in the bucket at the end of the cycle) > slightly shifting the bucket what is "slightly"? with respect to what? I moved the bucket in relation to the centreline of the stockpile (Image 2) and re-run the simulations and compare the results (cycle time and payload) with those from previous simulations. for the smaller particle sizes (100, 200, 300 mm) the difference was less than 3% while for the 400mm particles the difference between the results was more than 40%. I have been advised that using large particles in DEM results in the noise in the output and I do not quite understand why. If that is the case then how should we simulate phenomenon with large particle sizes? > the error was huge error of what? -- 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 #699075]: Error after launching the program
Question #699075 on Yade changed: https://answers.launchpad.net/yade/+question/699075 Status: Needs information => Solved Przemek confirmed that the question is solved: It works. -- 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 #699075]: Error after launching the program
Question #699075 on Yade changed: https://answers.launchpad.net/yade/+question/699075 Przemek posted a new comment: Hi Karol, I don't load saved simulation. I started new one. But like Jan suggested, I make fresh cmake and now it works. Thanks! Przemek -- 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 #699075]: Error after launching the program
Question #699075 on Yade changed: https://answers.launchpad.net/yade/+question/699075 Karol Brzezinski requested more information: Does your script try to load Yade simulation saved by different compilation of Yade? If so, it probably won't work. Prepare a new save with current version. Cheers, Karol -- 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 #699044]: How to set normal and tangential stiffnesse?
Question #699044 on Yade changed: https://answers.launchpad.net/yade/+question/699044 Summary changed to: How to set normal and tangential stiffnesse? -- 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 #699044]: How to set normal and tangential stiffnesse?
Question #699044 on Yade changed: https://answers.launchpad.net/yade/+question/699044 Robert Caulk posted a new comment: Please discontinue using foreign characters for the titles of your questions (I guess this is the 3rd or 4th time you have done this). The knowledge base is English based, and therefore foreign characters for titles is not searchable for other users. Thank you. -- 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 #699072]: About the examples/ThermalEngine
Question #699072 on Yade changed: https://answers.launchpad.net/yade/+question/699072 Status: Answered => Open Ziyu Wang is still having a problem: Thanks a lot Robert! >>Will you please install the latest source code version? You appear to have installed a snapshot from mid-March. Yes,I also noticed that.As you suggested[1], I used the following command: cd trunk git checkout -b working_state 61c90697 cd ../build cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk make -j4 install And then the version changes to 2021-03-16. I compiled it from the source code again. The version is yade-2021-09-28.git-52f0c5a.But when I run the original script (unchanged),the same problem still exists... >>Sphere size and distribution changes the maximum allowable timestep for numerical stability. If you decrease sphere size, you will need to decrease O.dt to maintain stability. Ok,I will decrease O.dt and provide timely feedback. -- 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 #699075]: Error after launching the program
Question #699075 on Yade changed: https://answers.launchpad.net/yade/+question/699075 Przemek posted a new comment: Ok, I will do it. > Could you share them? Ofcourse, but currently I'm working on them. So maybe it will be better to share them after validation and verification :) -- 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 #699075]: Error after launching the program
Question #699075 on Yade changed: https://answers.launchpad.net/yade/+question/699075 Jan Stránský requested more information: One option is to try fresh cmake / make process (from scratch). > I'm working only on my files with new laws. Could you share them? Cheers Jan -- 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 #699075]: Error after launching the program
Question #699075 on Yade changed: https://answers.launchpad.net/yade/+question/699075 Przemek posted a new comment: Hi, it is compiled Yade (if you remember I'm trying to use DEM in my thesis :) ) Right now I can't start yade alone. It's wierd... I'm working only on my files with new laws. But earlier it worked correctly, and now... error. > These errors comes from wrongly linked executable after compilation, meaning that the program requires Gl1_CpmPhys, but it does not know what it is (it was compiled, but not linked correctly). But where I should change the path. I don't change any headers before the last compiling. BR Przemek -- 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 #699075]: Error after launching the program
Question #699075 on Yade changed: https://answers.launchpad.net/yade/+question/699075 Status: Open => Needs information Jan Stránský requested more information: Hello, please provide more information [1], like if it is package or compiled Yade, if compiled how did you compile it etc. > after launching the simulation. what is "the simulation"? can you start yade alone? Under what circumstances the error occures? > earlier it worked. What does "earlier" mean? Did you do any changes to the program or system? > undefined symbol: _ZTVN4yade11Gl1_CpmPhysE These errors comes from wrongly linked executable after compilation, meaning that the program requires Gl1_CpmPhys, but it does not know what it is (it was compiled, but not linked correctly). Cheers Jan -- 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 #699070]: Effect of particle size on noise in the results
Question #699070 on Yade changed: https://answers.launchpad.net/yade/+question/699070 Status: Open => Needs information Jan Stránský requested more information: Hello, > I am new to DEM and I have very little experience with YADE and DEM welcome :-) please read [1] and provide (much) more information, ideally also a MWE if possible. > I am simulating ... a bucket ... a stockpile ... What is "a bucket" and "a stockpile"? What shape do they have? What are they composed from (spheres, facets, ...)? What is their mutual sizes and mutual sizes of the components? Are the components regular or not? ... ? ... ? > when I use large particle sizes What is "large", large with respect to what? 300-400mm alone is useless information... > the results are noisy What is "the result"? Positions, velocities, energies? Numerical result or visual state? ... ? > slightly shifting the bucket what is "slightly"? with respect to what? > the error was huge error of what? Cheers Jan [1] https://www.yade-dem.org/wiki/Howtoask -- 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 #699075]: Error after launching the program
New question #699075 on Yade: https://answers.launchpad.net/yade/+question/699075 Hi, I have a problem with some kind of error after launching the simulation. Welcome to Yade 2021-04-06.git-54b855f Using python version: 3.8.10 (default, Sep 28 2021, 16:10:42) [GCC 9.3.0] Traceback (most recent call last): File "/home/przemek/DEMlab/install/bin/yade", line 151, in import yade File "/home/przemek/DEMlab/install/lib/x86_64-linux-gnu/yade-2021-04-06.git-54b855f/py/yade/__init__.py", line 75, in from yade import boot ImportError: /home/przemek/DEMlab/install/lib/x86_64-linux-gnu/yade-2021-04-06.git-54b855f/libdem.so: undefined symbol: _ZTVN4yade11Gl1_CpmPhysE I don't know why it appear, because earlier it worked. Do you have any suggestions? BR Przemek -- 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 #699072]: About the examples/ThermalEngine
Question #699072 on Yade changed: https://answers.launchpad.net/yade/+question/699072 Robert Caulk proposed the following answer: Increasing sphere number in the same geometrical domain size, means smaller spheres. Smaller spheres means smaller characteristic lengths for the system. Smaller char. lengths means smaller allowable timestep. Please refer to this discussion for more details: https://answers.launchpad.net/yade/+question/698948 Cheers, Robert -- 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 #698948]: Stability of advection modeling by ThermalEngine
Question #698948 on Yade changed: https://answers.launchpad.net/yade/+question/698948 Robert Caulk proposed the following answer: Hey Zoheir, The version that you have installed is actually an *earlier* version than the branch you were using. Best to start using a *later* version so as to keep up with bug fixes etc. For example, I am using the latest, it is 52f0c5a7, but installing it is as simple as following these instructions [1]. >>Would you be able to try this one more time with rMean=0.001 on your machine? I would really appreciate your help Yes, it works when I decrease the timestep, as expected. The magnitude of timestep decrease depends on the seed and packing - we are sampling a uniform particle distribution [0.001+/-0.00033] 100 times. So sometimes we may get a tiny sphere other times we may not. That has significant impact on stability as I will teach to you below. (btw, we do not have the same seed values since we are on separate computers.) So you can change seed to demonstrate that process. I think it will help you for me to review to you directly the fluid conduction scheme: All particles are triangulated to create a connected set of tetrahedra. Each tetrahedron has 4 neighbors, and with those 4 neighbors, it shares 1 facet each. The fluid conduction is computed using the fluid area (A) of the incident facet divided by the distance between the two neighboring tetrahedra centers (L). Fluid area is simply the area of the facet not consumed by a sphere. Please refer to our paper for visualization of these geometries. So we have: q_12 = k_12 * A_12/L_12 * (T1 - T2) As we have discussed at length, the time step depends on this "diffusion coefficient" kA/L. As that increases, the allowable timestep decreases. So what does this mean? If the area is big, the timestep is small. If L is small, the timestep is small, if k is big, the timestep is small. We can refer to A/L as a characteristic length scale of the problem. When you start adding a wide distribution of spheres (rRelFuzz=0.33), you start to play with these geometries in the triangulation indirectly. Which means you are adjusting your maximum allowable timestep. So if you are constrained by the timestep of 1e-3, but you insist on decreasing the characteristic length scale of the fluid conduction scheme (decreasing sphere size), then you need to make some sacrifices elsewhere. At least, you can demonstrate this is the root of your instability by manually controlling the diffusion coefficient via python: thermal.minimumFluidCondDist=rMean thermal.fluidConductionAreaFactor=0.1 This means you have a fluid area that is anomalously large compared to the rest of your triangulation, or a length that is anomalously small. I leave it to you to play with these factors to determine which one it is. By the way, depending on the sensitivity of the triangulation (it can be quite sensitive when you have a wide range of vertex weights (sphere radii) ), you need to isolate the problem from any sort of external stochasticity such as parallelized compaction such as you are showing here. You have a slightly different triangulation each time (even using seed in make cloud). Thus, best practice is to export the packing and then import the identical packing each time. Cheers, Robert [1]https://yade-dem.org/doc/installation.html#source-code -- 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 #698948]: Stability of advection modeling by ThermalEngine
Question #698948 on Yade changed: https://answers.launchpad.net/yade/+question/698948 Robert Caulk proposed the following answer: Hey Zoheir, The version that you have installed is actually an *earlier* version than the branch you were using. Best to start using a *later* version so as to keep up with bug fixes etc. For example, I am using the latest, it is 52f0c5a7, but installing it is as simple as following these instructions [1]. >>Would you be able to try this one more time with rMean=0.001 on your machine? I would really appreciate your help Yes, it works when I decrease the timestep, as expected. The magnitude of timestep decrease depends on the seed and packing - we are sampling a uniform particle distribution [0.001+/-0.00033] 100 times. So sometimes we may get a tiny sphere other times we may not. That has significant impact on stability as I will teach to you below. (btw, we do not have the same seed values since we are on separate computers.) So you can change seed to demonstrate that process. I think it will help you for me to review to you directly the fluid conduction scheme: All particles are triangulated to create a connected set of tetrahedra. Each tetrahedron has 4 neighbors, and with those 4 neighbors, it shares 1 facet each. The fluid conduction is computed using the fluid area (A) of the incident facet divided by the distance between the two neighboring tetrahedra centers (L). Fluid area is simply the area of the facet not consumed by a sphere. Please refer to our paper for visualization of these geometries. So we have: q_12 = k_12 * A_12/L_12 * (T1 - T2) As we have discussed at length, the time step depends on this "diffusion coefficient" kA/L. As that increases, the allowable timestep decreases. So what does this mean? If the area is big, the timestep is small. If L is small, the timestep is small, if k is big, the timestep is small. We can refer to A/L as a characteristic length scale of the problem. When you start adding a wide distribution of spheres (rRelFuzz=0.33), you start to play with these geometries in the triangulation indirectly. Which means you are adjusting your maximum allowable timestep. So if you are constrained by the timestep of 1e-3, but you insist on decreasing the characteristic length scale of the fluid conduction scheme (decreasing sphere size), then you need to make some sacrifices elsewhere. At least, you can demonstrate this is the root of your instability by manually controlling the diffusion coefficient via python: thermal.minimumFluidCondDist=rMean thermal.fluidConductionAreaFactor=0.1 This means you have a fluid area that is anomalously large compared to the rest of your triangulation, or a length that is anomalously small. I leave it to you to play with these factors to determine which one it is. By the way, depending on the sensitivity of the triangulation (it can be quite sensitive when you have a wide range of vertex weights (sphere radii) ), you need to isolate the problem from any sort of external stochasticity such as parallelized compaction such as you are showing here. You have a slightly different triangulation each time (even using seed in make cloud). Thus, best practice is to export the packing and then import the identical packing each time. Cheers, Robert [1]https://yade-dem.org/doc/installation.html#source-code -- 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 #699030]: How to set the particle size when generating particles
Question #699030 on Yade changed: https://answers.launchpad.net/yade/+question/699030 Status: Open => Needs information Jan Stránský requested more information: > particle gradation curves is it particle size distribution? On horizontal axis size, on vertical axis % passing? If yes, then read [1] and focus on psdSizes, psdCumm, "psdSizes and psdCumm, two arrays specifying points of the particle size distribution function" etc. If no, please be more specific. Cheers Jan -- 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 #699072]: About the examples/ThermalEngine
Question #699072 on Yade changed: https://answers.launchpad.net/yade/+question/699072 Status: Open => Answered Robert Caulk proposed the following answer: Hello, >>1.When I run the original script (unchanged), the problem is the same as before: plot is blank and body.State.Temp = Nan. Will you please install the latest source code version? You appear to have installed a snapshot from mid-March. >>So I guess the problem has something to do with the number of spheres? Sphere size and distribution changes the maximum allowable timestep for numerical stability. If you decrease sphere size, you will need to decrease O.dt to maintain stability. Cheers, Robert -- 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 #699073]: Where to buy Adderall online
Question #699073 on Yade changed: https://answers.launchpad.net/yade/+question/699073 Status: Open => Invalid Jan Stránský rejected the question: spam -- 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 #699073]: Where to buy Adderall online
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Re: [Yade-users] [Question #699030]: How to set the particle size when generating particles
Question #699030 on Yade changed: https://answers.launchpad.net/yade/+question/699030 Status: Answered => Open 黎犴dada is still having a problem: Thank you very much for your reply! I still haven't solved my problem. I have carefully read the link you provided, but I still haven't come up with a method that can be incorporated into my existing particle grading -- 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
