Re: [Yade-users] [Question #670765]: negative volume for an ordinary pore
Question #670765 on Yade changed: https://answers.launchpad.net/yade/+question/670765 Status: Answered => Solved Zhang Wenyue confirmed that the question is solved: Thanks Robert Caulk, that solved my question. -- 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 #670765]: negative volume for an ordinary pore
Question #670765 on Yade changed: https://answers.launchpad.net/yade/+question/670765 Status: Open => Answered Robert Caulk proposed the following answer: >> I wonder whether there is a method which can adjust dt automatically. Probably! If you determine such a method I encourage you to share with the community. >> Can I just ignore the warning? Will it have any negative effect on the simulation? Here is the origin of the warning [1], looks like the author is using a triple product to evaluate each cell's volume [2] so the pseudoscalar output needs to be signed [3]. In other words, the volume calc may yield a negative value despite being perfectly safe. Hence the "should still be safe". However, in your case you are likely seeing this as a result of the large particle size mismatch in your simulation and the fast- moving particles. I think this combination results in very acute tetrahedral angles and if these particles move faster than the triangulation updates, they end up easily inverting themselves, resulting in a negative triple product. You are still getting the correct volume of a pore represented by the locations of those particles, but the forces are probably pretty inaccurate since the triangulation is outdated. If you are scared of this you could try updating the triangulation more frequently with meshUpdateInterval. [1]https://github.com/yade/trunk/blob/master/pkg/pfv/FlowEngine.ipp.in#L629 [2]https://github.com/yade/trunk/blob/master/pkg/pfv/FlowEngine.ipp.in#L628 [3]https://github.com/yade/trunk/blob/master/pkg/pfv/FlowEngine.ipp.in#L630 -- 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 #670765]: negative volume for an ordinary pore
Question #670765 on Yade changed: https://answers.launchpad.net/yade/+question/670765 Status: Solved => Open Zhang Wenyue is still having a problem: Dear Robert, I try O.dt=0.1e-4. At first it performs well, but when I run long enough, the warning of negative volume still appears. I wonder whether there is a method which can adjust dt automatically. This time the program didn't crash. Can I just ignore the warning? Will it have any negative effect on the simulation? Or is there any method can adjust the timestep automatically so that the warning won't show up? Thanks -- 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 #670765]: negative volume for an ordinary pore
Question #670765 on Yade changed: https://answers.launchpad.net/yade/+question/670765 Status: Answered => Solved Zhang Wenyue confirmed that the question is solved: Thanks Robert Caulk, that solved my question. -- 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 #670765]: negative volume for an ordinary pore
Question #670765 on Yade changed: https://answers.launchpad.net/yade/+question/670765 Robert Caulk proposed the following answer: Hello, You have two problems that require two solutions. One of your problems is an interesting phenomenon that needs to be documented, so I went ahead and answered Bruno's question for you ;-) << First problem >> negative volume for ordinary pore: Example reply to Bruno: I notice that when I add the small particles to the script, I get this error. But when I only use the large particles, the script is functional. Solution: Reduce the time step. Smaller particles require smaller time steps. Try an order of magnitude less: O.dt=0.1e-4 << Second problem >> Vh==NULL!!: Example reply to Bruno: When I use stressMask=7 (triaxialStress goals) with the Z-direction pressure gradient (flow.bndCondValue=[0,0,0,0,100,0], I notice the packing drifts in the Z-direction until the particles become uncontained and fly away, resulting in the Vh==NULL!! error. Explanation: Your imposed pressure gradient is pushing on the particles in the Z-direction, those particles are pushing on your walls in the Z-direction. You commanded your walls to maintain constant stress, so they move to accommodate the changing stress. Solution: The problem can be corrected by locking one of the walls [2] associated with the pressure boundary condition: triax.wall_back_activated=False Cheers, Robert [1]https://answers.launchpad.net/yade/+question/634175 [2]https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.TriaxialStressController.wall_back_activated -- 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 #670765]: negative volume for an ordinary pore
Question #670765 on Yade changed: https://answers.launchpad.net/yade/+question/670765 Status: Open => Answered Bruno Chareyre proposed the following answer: Hi, could you describe in which way you modified the example script to make it disfunctional? -- 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 #670765]: negative volume for an ordinary pore
Question #670765 on Yade changed: https://answers.launchpad.net/yade/+question/670765 Zhang Wenyue posted a new comment: I have noticed a similar question: https://answers.launchpad.net/yade/+question/634175 I don't understand the answer in that question. Can anyone give me more help? I also got the following error: - .. 1048 : Vh==NULL!! id=1048 Point=21.9765 -0.29241 -8.71654 rad=0.03 1049 : Vh==NULL!! id=1049 Point=-nan -nan -nan rad=0.03 1050 : Vh==NULL!! id=1050 Point=17.5632 13.8312 -3.46853 rad=0.03 1051 : Vh==NULL!! id=1051 Point=47969.9 27856.3 55384.9 rad=0.03 1052 : Vh==NULL!! id=1052 Point=1.07385 -0.399759 -1.86005 rad=0.03 1053 : Vh==NULL!! id=1053 Point=-nan -nan -nan rad=0.03 1054 : Vh==NULL!! id=1054 Point=-136772 298537 61692.5 rad=0.03 1055 : Vh==NULL!! id=1055 Point=-nan -nan -nan rad=0.03 Vh==NULL!! id=1054 Point=-13046.5 28479.2 5889.76 rad=0.03 CHOLMOD error: invalid xtype. file: ../Cholesky/cholmod_analyze.c line: 431 CHOLMOD error: argument missing. file: ../Cholesky/cholmod_factorize.c line: 121 Segmentation fault (core dumped) -- 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 #670765]: negative volume for an ordinary pore
Question #670765 on Yade changed: https://answers.launchpad.net/yade/+question/670765 Status: Answered => Open Zhang Wenyue is still having a problem: Sorry, the script should be like this. I find that the small particles did move slowly, which means the engine works. But the warning of negative volume for an ordinary pore still appear. from yade import pack num_spheres=1000# number of spheres young=1e6 compFricDegree = 3 # initial contact friction during the confining phase finalFricDegree = 30 # contact friction during the deviatoric loading mn,mx=Vector3(0,0,0),Vector3(2,2,6) # corners of the initial packing O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),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=0.3,rRelFuzz=0,num=50,periodic=False) sp.makeCloud(mn,mx,rMean=0.03,rRelFuzz=0,num=900,periodic=False) sp.toSimulation(material='spheres') triax=TriaxialStressController( thickness = 0, stressMask = 7, max_vel = 0.005, internalCompaction=0, # If true the confining pressure is generated by growing particles wall_bottom_activated=False ) newton=NewtonIntegrator(damping=0.2) 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()],label="iloop" ), FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8), triax, newton ] triax.goal1=triax.goal2=triax.goal3=-1 while 1: O.run(1000, True) unb=unbalancedForce() if unb<0.001 and abs(-1-triax.meanStress)/1<0.001: break setContactFriction(radians(finalFricDegree)) ## __ Oedometer section _ triax.stressMask=7 triax.goal1=triax.goal2=triax.goal3=-1 #B. Activate flow engine and set boundary conditions in order to get permeability flow.dead=0 flow.defTolerance=0.3 flow.meshUpdateInterval=200 flow.useSolver=3 flow.permeabilityFactor=1 flow.viscosity=10 flow.bndCondIsPressure=[0,0,0,0,1,1] flow.bndCondValue=[0,0,0,0,100,0] flow.boundaryUseMaxMin=[0,0,0,0,0,0] O.dt=0.1e-3 O.dynDt=False newton.damping=0 -- 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 #670765]: negative volume for an ordinary pore
Question #670765 on Yade changed: https://answers.launchpad.net/yade/+question/670765 Status: Open => Answered Bruno Chareyre proposed the following answer: Hi, could you describe in which way you modified the example script to make it disfunctional? -- 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 #670765]: negative volume for an ordinary pore
New question #670765 on Yade: https://answers.launchpad.net/yade/+question/670765 Hi, I'm working on DEM-PFV coupling and get some problems. 1)When I run the simulation, I get such warning: negative volume for an ordinary pore (temp warning, should still be safe) 2)I start the simulation through the controller and inspect it in the 3D view, I find that the small particles are not moving under the fluid force. The FlowEngine is added before the newton integrator, why doesn't the fluid force acting on the particles? Can anyone give me some suggestion? Thanks a lot. I'm running Yade 2018.02b, Ubuntu 18.04. My code is shown as follow: from yade import pack num_spheres=1000# number of spheres young=1e6 compFricDegree = 3 # initial contact friction during the confining phase finalFricDegree = 30 # contact friction during the deviatoric loading mn,mx=Vector3(0,0,0),Vector3(2,2,6) # corners of the initial packing O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),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=0.3,rRelFuzz=0,num=100,periodic=False) sp.makeCloud(mn,mx,rMean=0.03,rRelFuzz=0,num=900,periodic=False) sp.toSimulation(material='spheres') triax=TriaxialStressController( thickness = 0, stressMask = 7, max_vel = 0.005, internalCompaction=0, # If true the confining pressure is generated by growing particles wall_bottom_activated=False ) newton=NewtonIntegrator(damping=0.2) 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()],label="iloop" ), FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8), triax, newton ] triax.goal1=triax.goal2=triax.goal3=-1 while 1: O.run(1000, True) unb=unbalancedForce() if unb<0.001 and abs(-1-triax.meanStress)/1<0.001: break setContactFriction(radians(finalFricDegree)) ## __ Oedometer section _ triax.stressMask=7 triax.goal1=triax.goal2=triax.goal3=-1 #B. Activate flow engine and set boundary conditions in order to get permeability flow.dead=0 flow.defTolerance=0.3 flow.meshUpdateInterval=200 flow.useSolver=3 flow.permeabilityFactor=1 flow.viscosity=10 flow.bndCondIsPressure=[0,0,0,0,1,1] flow.bndCondValue=[0,0,0,0,10,0] flow.boundaryUseMaxMin=[0,0,0,0,0,0] O.dt=0.1e-3 O.dynDt=False newton.damping=0 == Best, Zhang Wenyue -- 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
