subject:"\[Yade\-dev\] \: Add damping coefficient to material"

Re: [Yade-dev] : Add damping coefficient to material

2012-01-23 Thread Chiara


On 23/01/12 00:12, Klaus Thoeni wrote:

Hi Bruno, hi Anton,

I think density scaling is not what I am looking for since I am interested in
real dynamic simulations. I need different damping parameters in
NewtonIntegrator for the block and the mesh. I have to consider free flight
under gravity so damping=0 (and I am interested in the real flight time). For
the mesh I have to consider additional energy absorption which is not
considered in my model via damping.
If you are not after any density scaling, why damping in 
NewtonIntegrator should be acceptable in a realistic dynamic situation? 
Would not be easier/more meaningful for you to implement damping inside 
your contact model? Sorry, just curious.

Chiara


It is similar to b_damp() in PFC which is used to remove damping for certain
particle. I implemented it the same way now. The state has a member which is
true by default which means that damping is used. It can be set to false and
damping=0 will be used for this particle. So basically damping in
NewtonIntegrator can be activated and deactivated for individual particles.

@Anton: It has to be checked for all particles.

Here is the diff of my latest implementation, tell me what you think:

=== modified file core/State.hpp
--- core/State.hpp  2011-02-14 08:05:09 +
+++ core/State.hpp  2012-01-22 23:56:31 +
@@ -59,7 +59,8 @@
((Vector3r,inertia,Vector3r::Zero(),,Inertia of associated 
body, in
local coordinate system.))
((Vector3r,refPos,Vector3r::Zero(),,Reference position))
((Quaternionr,refOri,Quaternionr::Identity(),,Reference 
orientation))
-   ((unsigned,blockedDOFs,,,[Will be overridden])),
+   ((unsigned,blockedDOFs,,,[Will be overridden]))
+   ((bool,isDamped,true,,Damping in :yref:`Newtonintegrator` can 
be
deactivated for individual particles by setting this variable to FALSE. E.g.
damping is inappropriate for particles in free flight under gravity but it
might still be applicable to other particles in the same simulation.)),
/* additional initializers */
((pos,se3.position))
((ori,se3.orientation)),

=== modified file pkg/dem/NewtonIntegrator.cpp
--- pkg/dem/NewtonIntegrator.cpp2011-11-30 17:39:33 +
+++ pkg/dem/NewtonIntegrator.cpp2012-01-22 23:56:31 +
@@ -11,17 +11,18 @@
  #includeyade/pkg/dem/Clump.hpp
  #includeyade/pkg/common/VelocityBins.hpp
  #includeyade/lib/base/Math.hpp

  YADE_PLUGIN((NewtonIntegrator));
  CREATE_LOGGER(NewtonIntegrator);

  // 1st order numerical damping
-void NewtonIntegrator::cundallDamp1st(Vector3r  force, const Vector3r  vel){
-   for(int i=0; i3; i++) force[i]*=1-damping*Mathr::Sign(force[i]*vel[i]);
+void NewtonIntegrator::cundallDamp1st(Vector3r  force, const Vector3r  vel,
const Real  dampcoeff){
+   for(int i=0; i3; i++) 
force[i]*=1-dampcoeff*Mathr::Sign(force[i]*vel[i]);
  }
  // 2nd order numerical damping
-void NewtonIntegrator::cundallDamp2nd(const Real  dt, const Vector3r  force,
const Vector3r  vel, Vector3r  accel){
-   for(int i=0; i3; i++) accel[i]*= 1 - damping*Mathr::Sign (
force[i]*(vel[i] + 0.5*dt*accel[i]) );
+void NewtonIntegrator::cundallDamp2nd(const Real  dt, const Vector3r  force,
const Vector3r  vel, Vector3r  accel, const Real  dampcoeff){
+   for(int i=0; i3; i++) accel[i]*= 1 - dampcoeff*Mathr::Sign (
force[i]*(vel[i] + 0.5*dt*accel[i]) );
  }

  Vector3r NewtonIntegrator::computeAccel(const Vector3r  force, const Real
mass, int blockedDOFs){
@@ -39,11 +40,13 @@

  void NewtonIntegrator::updateEnergy(const shared_ptrBody  b, const State*
state, const Vector3r  fluctVel, const Vector3r  f, const Vector3r  m){
assert(b-isStandalone() || b-isClump());
-   // always positive dissipation, by-component: |F_i|*|v_i|*damping*dt (|
T_i|*|ω_i|*damping*dt for rotations)
-   if(damping!=0.){
-   scene-energy-

add(fluctVel.cwise().abs().dot(f.cwise().abs())*damping*scene-
dt,nonviscDamp,nonviscDampIx,/*non-incremental*/false);

+   // check if damping for this body is activated
+   Real dampcoeff=(state-isDamped ? damping : 0);
+   // always positive dissipation, by-component: |F_i|*|v_i|*dampcoeff*dt 
(|
T_i|*|ω_i|*dampcoeff*dt for rotations)
+   if(dampcoeff!=0.){
+   scene-energy-

add(fluctVel.cwise().abs().dot(f.cwise().abs())*dampcoeff*scene-
dt,nonviscDamp,nonviscDampIx,/*non-incremental*/false);

// when the aspherical integrator is used, torque is damped 
instead of
ang acceleration; this code is only approximate
-   scene-energy-add(state-

angVel.cwise().abs().dot(m.cwise().abs())*damping*scene-
dt,nonviscDamp,nonviscDampIx,false);

+   scene-energy-add(state-

angVel.cwise().abs().dot(m.cwise().abs())*dampcoeff*scene-
dt,nonviscDamp,nonviscDampIx,false);

}
// kinetic energy
Real

Re: [Yade-dev] : Add damping coefficient to material

2012-01-23 Thread Klaus Thoeni

Hi Chiara,

thanks for your comment. I am not after viscous damping either. But I think 
the current implementation does exactly what I want, it's the same as the PFC 
option b_damp(). So I can deactivate the damping coefficient for individual 
bodies.

I can commit the code if anyone is interested , after the diff has been 
approved ;-)

Klaus

On Mon, 23 Jan 2012 08:44:02 PM Chiara wrote:
 On 23/01/12 00:12, Klaus Thoeni wrote:
  Hi Bruno, hi Anton,
  
  I think density scaling is not what I am looking for since I am
  interested in real dynamic simulations. I need different damping
  parameters in NewtonIntegrator for the block and the mesh. I have to
  consider free flight under gravity so damping=0 (and I am interested in
  the real flight time). For the mesh I have to consider additional energy
  absorption which is not considered in my model via damping.
 
 If you are not after any density scaling, why damping in
 NewtonIntegrator should be acceptable in a realistic dynamic situation?
 Would not be easier/more meaningful for you to implement damping inside
 your contact model? Sorry, just curious.
 Chiara
 
  It is similar to b_damp() in PFC which is used to remove damping for
  certain particle. I implemented it the same way now. The state has a
  member which is true by default which means that damping is used. It can
  be set to false and damping=0 will be used for this particle. So
  basically damping in NewtonIntegrator can be activated and deactivated
  for individual particles.
  
  @Anton: It has to be checked for all particles.
  
  Here is the diff of my latest implementation, tell me what you think:
  
  === modified file core/State.hpp
  --- core/State.hpp  2011-02-14 08:05:09 +
  +++ core/State.hpp  2012-01-22 23:56:31 +
  @@ -59,7 +59,8 @@
  
  ((Vector3r,inertia,Vector3r::Zero(),,Inertia of associated 
  body, 
in
  
  local coordinate system.))
  
  ((Vector3r,refPos,Vector3r::Zero(),,Reference position))
  ((Quaternionr,refOri,Quaternionr::Identity(),,Reference
  orientation))
  
  -   ((unsigned,blockedDOFs,,,[Will be overridden])),
  +   ((unsigned,blockedDOFs,,,[Will be overridden]))
  +   ((bool,isDamped,true,,Damping in :yref:`Newtonintegrator` can 
  be
  deactivated for individual particles by setting this variable to FALSE.
  E.g. damping is inappropriate for particles in free flight under gravity
  but it might still be applicable to other particles in the same
  simulation.)),
  
  /* additional initializers */
  
  ((pos,se3.position))
  ((ori,se3.orientation)),
  
  === modified file pkg/dem/NewtonIntegrator.cpp
  --- pkg/dem/NewtonIntegrator.cpp2011-11-30 17:39:33 +
  +++ pkg/dem/NewtonIntegrator.cpp2012-01-22 23:56:31 +
  @@ -11,17 +11,18 @@
  
#includeyade/pkg/dem/Clump.hpp
#includeyade/pkg/common/VelocityBins.hpp
#includeyade/lib/base/Math.hpp

YADE_PLUGIN((NewtonIntegrator));
CREATE_LOGGER(NewtonIntegrator);

// 1st order numerical damping
  
  -void NewtonIntegrator::cundallDamp1st(Vector3r  force, const Vector3r 
  vel){ - for(int i=0; i3; i++)
  force[i]*=1-damping*Mathr::Sign(force[i]*vel[i]); +void
  NewtonIntegrator::cundallDamp1st(Vector3r  force, const Vector3r  vel,
  const Real  dampcoeff){
  +   for(int i=0; i3; i++)
  force[i]*=1-dampcoeff*Mathr::Sign(force[i]*vel[i]);
  
}
// 2nd order numerical damping
  
  -void NewtonIntegrator::cundallDamp2nd(const Real  dt, const Vector3r 
  force, const Vector3r  vel, Vector3r  accel){
  -   for(int i=0; i3; i++) accel[i]*= 1 - damping*Mathr::Sign (
  force[i]*(vel[i] + 0.5*dt*accel[i]) );
  +void NewtonIntegrator::cundallDamp2nd(const Real  dt, const Vector3r 
  force, const Vector3r  vel, Vector3r  accel, const Real  dampcoeff){
  +   for(int i=0; i3; i++) accel[i]*= 1 - dampcoeff*Mathr::Sign (
  force[i]*(vel[i] + 0.5*dt*accel[i]) );
  
}

Vector3r NewtonIntegrator::computeAccel(const Vector3r  force, const
Real
  
  mass, int blockedDOFs){
  @@ -39,11 +40,13 @@
  
void NewtonIntegrator::updateEnergy(const shared_ptrBody  b, const
State*
  
  state, const Vector3r  fluctVel, const Vector3r  f, const Vector3r 
  m){
  
  assert(b-isStandalone() || b-isClump());
  
  -   // always positive dissipation, by-component: |F_i|*|v_i|*damping*dt 
(|
  T_i|*|ω_i|*damping*dt for rotations)
  -   if(damping!=0.){
  -   scene-energy-
  
  add(fluctVel.cwise().abs().dot(f.cwise().abs())*damping*scene-
  dt,nonviscDamp,nonviscDampIx,/*non-incremental*/false);
  
  +   // check if damping for this body is activated
  +   Real dampcoeff=(state-isDamped ? damping : 0);
  +   // always positive dissipation, by-component: |F_i|*|v_i|*dampcoeff*dt
  (| T_i|*|ω_i|*dampcoeff*dt for rotations)
  +   if(dampcoeff!=0.){
  +   scene-energy-

Re: [Yade-dev] : Add damping coefficient to material

2012-01-23 Thread Bruno Chareyre

Ok, I understand.
I like your diff more than the previous one. :)
Still one suggestion: this additional parameter in the damping functions
is useless:

+   
cundallDamp2nd(dt,m,state-angVel,angAccel,dampcoeff);

In your code, dampCoeff will be either Newton::damping or zero.
So, it would be better to just write this, avoiding the function call
and additional parameter:

if (state-isDamped) cundallDamp2nd(dt,m,state-angVel,angAccel)

Then I agree to commit.

Bruno




On 23/01/12 11:48, Klaus Thoeni wrote:
 Hi Chiara,

 thanks for your comment. I am not after viscous damping either. But I think 
 the current implementation does exactly what I want, it's the same as the PFC 
 option b_damp(). So I can deactivate the damping coefficient for individual 
 bodies.

 I can commit the code if anyone is interested , after the diff has been 
 approved ;-)

 Klaus

 On Mon, 23 Jan 2012 08:44:02 PM Chiara wrote:
 On 23/01/12 00:12, Klaus Thoeni wrote:
 Hi Bruno, hi Anton,

 I think density scaling is not what I am looking for since I am
 interested in real dynamic simulations. I need different damping
 parameters in NewtonIntegrator for the block and the mesh. I have to
 consider free flight under gravity so damping=0 (and I am interested in
 the real flight time). For the mesh I have to consider additional energy
 absorption which is not considered in my model via damping.
 If you are not after any density scaling, why damping in
 NewtonIntegrator should be acceptable in a realistic dynamic situation?
 Would not be easier/more meaningful for you to implement damping inside
 your contact model? Sorry, just curious.
 Chiara

 It is similar to b_damp() in PFC which is used to remove damping for
 certain particle. I implemented it the same way now. The state has a
 member which is true by default which means that damping is used. It can
 be set to false and damping=0 will be used for this particle. So
 basically damping in NewtonIntegrator can be activated and deactivated
 for individual particles.

 @Anton: It has to be checked for all particles.

 Here is the diff of my latest implementation, tell me what you think:

 === modified file core/State.hpp
 --- core/State.hpp  2011-02-14 08:05:09 +
 +++ core/State.hpp  2012-01-22 23:56:31 +
 @@ -59,7 +59,8 @@

 ((Vector3r,inertia,Vector3r::Zero(),,Inertia of associated 
 body, 
 in
 local coordinate system.))

 ((Vector3r,refPos,Vector3r::Zero(),,Reference position))
 ((Quaternionr,refOri,Quaternionr::Identity(),,Reference
 orientation))

 -   ((unsigned,blockedDOFs,,,[Will be overridden])),
 +   ((unsigned,blockedDOFs,,,[Will be overridden]))
 +   ((bool,isDamped,true,,Damping in :yref:`Newtonintegrator` can 
 be
 deactivated for individual particles by setting this variable to FALSE.
 E.g. damping is inappropriate for particles in free flight under gravity
 but it might still be applicable to other particles in the same
 simulation.)),

 /* additional initializers */
 
 ((pos,se3.position))
 ((ori,se3.orientation)),

 === modified file pkg/dem/NewtonIntegrator.cpp
 --- pkg/dem/NewtonIntegrator.cpp2011-11-30 17:39:33 +
 +++ pkg/dem/NewtonIntegrator.cpp2012-01-22 23:56:31 +
 @@ -11,17 +11,18 @@

   #includeyade/pkg/dem/Clump.hpp
   #includeyade/pkg/common/VelocityBins.hpp
   #includeyade/lib/base/Math.hpp
   
   YADE_PLUGIN((NewtonIntegrator));
   CREATE_LOGGER(NewtonIntegrator);
   
   // 1st order numerical damping

 -void NewtonIntegrator::cundallDamp1st(Vector3r  force, const Vector3r 
 vel){ - for(int i=0; i3; i++)
 force[i]*=1-damping*Mathr::Sign(force[i]*vel[i]); +void
 NewtonIntegrator::cundallDamp1st(Vector3r  force, const Vector3r  vel,
 const Real  dampcoeff){
 +   for(int i=0; i3; i++)
 force[i]*=1-dampcoeff*Mathr::Sign(force[i]*vel[i]);

   }
   // 2nd order numerical damping

 -void NewtonIntegrator::cundallDamp2nd(const Real  dt, const Vector3r 
 force, const Vector3r  vel, Vector3r  accel){
 -   for(int i=0; i3; i++) accel[i]*= 1 - damping*Mathr::Sign (
 force[i]*(vel[i] + 0.5*dt*accel[i]) );
 +void NewtonIntegrator::cundallDamp2nd(const Real  dt, const Vector3r 
 force, const Vector3r  vel, Vector3r  accel, const Real  dampcoeff){
 +   for(int i=0; i3; i++) accel[i]*= 1 - dampcoeff*Mathr::Sign (
 force[i]*(vel[i] + 0.5*dt*accel[i]) );

   }
   
   Vector3r NewtonIntegrator::computeAccel(const Vector3r  force, const
   Real

 mass, int blockedDOFs){
 @@ -39,11 +40,13 @@

   void NewtonIntegrator::updateEnergy(const shared_ptrBody  b, const
   State*

 state, const Vector3r  fluctVel, const Vector3r  f, const Vector3r 
 m){

 assert(b-isStandalone() || b-isClump());

 -   // always positive dissipation, by-component: |F_i|*|v_i|*damping*dt 
 (|
 T_i|*|ω_i|*damping*dt for rotations)
 -   if(damping!=0.){
 -   scene-energy-

Re: [Yade-dev] : Add damping coefficient to material

2012-01-23 Thread Anton Gladky

On Mon, Jan 23, 2012 at 10:44 AM, Chiara c.moden...@gmail.com wrote:
...

 If you are not after any density scaling, why damping in NewtonIntegrator
 should be acceptable in a realistic dynamic situation? Would not be
 easier/more meaningful for you to implement damping inside your contact
 model?

...

The bodies, which are not interact at the moment, will be skipped  in
this case, I think.
Agree with Bruno, This diff looks better.

Anton.

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Re: [Yade-dev] : Add damping coefficient to material

2012-01-23 Thread Klaus Thoeni

Hi guys,

thanks a lot for your suggestions. I just committed the code and I think it 
looks very good now.

Klaus

On Mon, 23 Jan 2012 11:08:59 PM Bruno Chareyre wrote:
 Ok, I understand.
 I like your diff more than the previous one. :)
 Still one suggestion: this additional parameter in the damping functions
 is useless:
 
 + 
 cundallDamp2nd(dt,m,state-angVel,angAccel,dampcoeff);
 
 In your code, dampCoeff will be either Newton::damping or zero.
 So, it would be better to just write this, avoiding the function call
 and additional parameter:
 
 if (state-isDamped) cundallDamp2nd(dt,m,state-angVel,angAccel)
 
 Then I agree to commit.
 
 Bruno
 
 On 23/01/12 11:48, Klaus Thoeni wrote:
  Hi Chiara,
  
  thanks for your comment. I am not after viscous damping either. But I
  think the current implementation does exactly what I want, it's the same
  as the PFC option b_damp(). So I can deactivate the damping coefficient
  for individual bodies.
  
  I can commit the code if anyone is interested , after the diff has been
  approved ;-)
  
  Klaus
  
  On Mon, 23 Jan 2012 08:44:02 PM Chiara wrote:
  On 23/01/12 00:12, Klaus Thoeni wrote:
  Hi Bruno, hi Anton,
  
  I think density scaling is not what I am looking for since I am
  interested in real dynamic simulations. I need different damping
  parameters in NewtonIntegrator for the block and the mesh. I have to
  consider free flight under gravity so damping=0 (and I am interested in
  the real flight time). For the mesh I have to consider additional
  energy absorption which is not considered in my model via damping.
  
  If you are not after any density scaling, why damping in
  NewtonIntegrator should be acceptable in a realistic dynamic situation?
  Would not be easier/more meaningful for you to implement damping inside
  your contact model? Sorry, just curious.
  Chiara
  
  It is similar to b_damp() in PFC which is used to remove damping for
  certain particle. I implemented it the same way now. The state has a
  member which is true by default which means that damping is used. It
  can be set to false and damping=0 will be used for this particle. So
  basically damping in NewtonIntegrator can be activated and deactivated
  for individual particles.
  
  @Anton: It has to be checked for all particles.
  
  Here is the diff of my latest implementation, tell me what you think:
  
  === modified file core/State.hpp
  --- core/State.hpp2011-02-14 08:05:09 +
  +++ core/State.hpp2012-01-22 23:56:31 +
  @@ -59,7 +59,8 @@
  
((Vector3r,inertia,Vector3r::Zero(),,Inertia of 
  associated body,
  
  in
  
  local coordinate system.))
  
((Vector3r,refPos,Vector3r::Zero(),,Reference 
  position))
((Quaternionr,refOri,Quaternionr::Identity(),,Reference
orientation))
  
  - ((unsigned,blockedDOFs,,,[Will be overridden])),
  + ((unsigned,blockedDOFs,,,[Will be overridden]))
  + ((bool,isDamped,true,,Damping in :yref:`Newtonintegrator` can 
  be
  deactivated for individual particles by setting this variable to FALSE.
  E.g. damping is inappropriate for particles in free flight under
  gravity but it might still be applicable to other particles in the
  same simulation.)),
  
/* additional initializers */

((pos,se3.position))
((ori,se3.orientation)),
  
  === modified file pkg/dem/NewtonIntegrator.cpp
  --- pkg/dem/NewtonIntegrator.cpp  2011-11-30 17:39:33 +
  +++ pkg/dem/NewtonIntegrator.cpp  2012-01-22 23:56:31 +
  @@ -11,17 +11,18 @@
  
#includeyade/pkg/dem/Clump.hpp
#includeyade/pkg/common/VelocityBins.hpp
#includeyade/lib/base/Math.hpp

YADE_PLUGIN((NewtonIntegrator));
CREATE_LOGGER(NewtonIntegrator);

// 1st order numerical damping
  
  -void NewtonIntegrator::cundallDamp1st(Vector3r  force, const
  Vector3r vel){ - for(int i=0; i3; i++)
  force[i]*=1-damping*Mathr::Sign(force[i]*vel[i]); +void
  NewtonIntegrator::cundallDamp1st(Vector3r  force, const Vector3r 
  vel, const Real  dampcoeff){
  + for(int i=0; i3; i++)
  force[i]*=1-dampcoeff*Mathr::Sign(force[i]*vel[i]);
  
}
// 2nd order numerical damping
  
  -void NewtonIntegrator::cundallDamp2nd(const Real  dt, const Vector3r
  force, const Vector3r  vel, Vector3r  accel){
  - for(int i=0; i3; i++) accel[i]*= 1 - damping*Mathr::Sign (
  force[i]*(vel[i] + 0.5*dt*accel[i]) );
  +void NewtonIntegrator::cundallDamp2nd(const Real  dt, const Vector3r
  force, const Vector3r  vel, Vector3r  accel, const Real  dampcoeff){
  + for(int i=0; i3; i++) accel[i]*= 1 - dampcoeff*Mathr::Sign (
  force[i]*(vel[i] + 0.5*dt*accel[i]) );
  
}

Vector3r NewtonIntegrator::computeAccel(const Vector3r  force, const
Real
  
  mass, int blockedDOFs){
  @@ -39,11 +40,13 @@
  
void

Re: [Yade-dev] : Add damping coefficient to material

2012-01-22 Thread Klaus Thoeni

Hi Bruno, hi Anton, 

I think density scaling is not what I am looking for since I am interested in 
real dynamic simulations. I need different damping parameters in 
NewtonIntegrator for the block and the mesh. I have to consider free flight 
under gravity so damping=0 (and I am interested in the real flight time). For 
the mesh I have to consider additional energy absorption which is not 
considered in my model via damping.

It is similar to b_damp() in PFC which is used to remove damping for certain 
particle. I implemented it the same way now. The state has a member which is 
true by default which means that damping is used. It can be set to false and 
damping=0 will be used for this particle. So basically damping in 
NewtonIntegrator can be activated and deactivated for individual particles.

@Anton: It has to be checked for all particles.

Here is the diff of my latest implementation, tell me what you think:

=== modified file core/State.hpp
--- core/State.hpp  2011-02-14 08:05:09 +
+++ core/State.hpp  2012-01-22 23:56:31 +
@@ -59,7 +59,8 @@
((Vector3r,inertia,Vector3r::Zero(),,Inertia of associated 
body, in 
local coordinate system.))
((Vector3r,refPos,Vector3r::Zero(),,Reference position))
((Quaternionr,refOri,Quaternionr::Identity(),,Reference 
orientation))
-   ((unsigned,blockedDOFs,,,[Will be overridden])),
+   ((unsigned,blockedDOFs,,,[Will be overridden]))
+   ((bool,isDamped,true,,Damping in :yref:`Newtonintegrator` can 
be 
deactivated for individual particles by setting this variable to FALSE. E.g. 
damping is inappropriate for particles in free flight under gravity but it 
might still be applicable to other particles in the same simulation.)),
/* additional initializers */
((pos,se3.position))
((ori,se3.orientation)),

=== modified file pkg/dem/NewtonIntegrator.cpp
--- pkg/dem/NewtonIntegrator.cpp2011-11-30 17:39:33 +
+++ pkg/dem/NewtonIntegrator.cpp2012-01-22 23:56:31 +
@@ -11,17 +11,18 @@
 #includeyade/pkg/dem/Clump.hpp
 #includeyade/pkg/common/VelocityBins.hpp
 #includeyade/lib/base/Math.hpp
 
 YADE_PLUGIN((NewtonIntegrator));
 CREATE_LOGGER(NewtonIntegrator);
 
 // 1st order numerical damping
-void NewtonIntegrator::cundallDamp1st(Vector3r force, const Vector3r vel){
-   for(int i=0; i3; i++) force[i]*=1-damping*Mathr::Sign(force[i]*vel[i]);
+void NewtonIntegrator::cundallDamp1st(Vector3r force, const Vector3r vel, 
const Real dampcoeff){
+   for(int i=0; i3; i++) 
force[i]*=1-dampcoeff*Mathr::Sign(force[i]*vel[i]);
 }
 // 2nd order numerical damping
-void NewtonIntegrator::cundallDamp2nd(const Real dt, const Vector3r force, 
const Vector3r vel, Vector3r accel){
-   for(int i=0; i3; i++) accel[i]*= 1 - damping*Mathr::Sign ( 
force[i]*(vel[i] + 0.5*dt*accel[i]) );
+void NewtonIntegrator::cundallDamp2nd(const Real dt, const Vector3r force, 
const Vector3r vel, Vector3r accel, const Real dampcoeff){
+   for(int i=0; i3; i++) accel[i]*= 1 - dampcoeff*Mathr::Sign ( 
force[i]*(vel[i] + 0.5*dt*accel[i]) );
 }
 
 Vector3r NewtonIntegrator::computeAccel(const Vector3r force, const Real 
mass, int blockedDOFs){
@@ -39,11 +40,13 @@
 
 void NewtonIntegrator::updateEnergy(const shared_ptrBody b, const State* 
state, const Vector3r fluctVel, const Vector3r f, const Vector3r m){
assert(b-isStandalone() || b-isClump());
-   // always positive dissipation, by-component: |F_i|*|v_i|*damping*dt (|
T_i|*|ω_i|*damping*dt for rotations)
-   if(damping!=0.){
-   scene-energy-
add(fluctVel.cwise().abs().dot(f.cwise().abs())*damping*scene-
dt,nonviscDamp,nonviscDampIx,/*non-incremental*/false);
+   // check if damping for this body is activated
+   Real dampcoeff=(state-isDamped ? damping : 0);
+   // always positive dissipation, by-component: |F_i|*|v_i|*dampcoeff*dt 
(|
T_i|*|ω_i|*dampcoeff*dt for rotations)
+   if(dampcoeff!=0.){
+   scene-energy-
add(fluctVel.cwise().abs().dot(f.cwise().abs())*dampcoeff*scene-
dt,nonviscDamp,nonviscDampIx,/*non-incremental*/false);
// when the aspherical integrator is used, torque is damped 
instead of 
ang acceleration; this code is only approximate
-   scene-energy-add(state-
angVel.cwise().abs().dot(m.cwise().abs())*damping*scene-
dt,nonviscDamp,nonviscDampIx,false);
+   scene-energy-add(state-
angVel.cwise().abs().dot(m.cwise().abs())*dampcoeff*scene-
dt,nonviscDamp,nonviscDampIx,false);
}
// kinetic energy
Real Etrans=.5*state-mass*fluctVel.squaredNorm();
@@ -106,9 +109,13 @@
YADE_PARALLEL_FOREACH_BODY_BEGIN(const shared_ptrBody b, 
scene-bodies)
{
// clump members are handled inside clumps
if(unlikely(b-isClumpMember())) continue;
-
+   
State*

Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Klaus Thoeni

Hi Anton,

I just had a look at py/tests/clump.py, that's the test which fails. I added 
this after line 60 (before NewtonIntegrator is called):

for b in O.bodies: print b.material

and that's what I get:

FrictMat instance at 0x1014c10
None

So the second body has no material. I think it's more a problem in the test. 
In a, lets say, real simulation the material always exists (or not?), so I am 
not sure if checking for the material makes sense and it would be quit 
inefficient.

However, I am not familiar with the testing stuff. Is there anyone who knows 
why the second body gives 'None' for the material?

Klaus

On Thu, 19 Jan 2012 06:31:09 PM Anton Gladky wrote:
   Real getDampCoeff() { return material-damping; };
 
 Can you check here a material existence?
 
 Anton
 
 On Thu, Jan 19, 2012 at 8:14 AM, Klaus Thoeni klaus.tho...@gmail.com 
wrote:
  Hi guys,
  
  can anyone help me on this?
  
  Klaus
  
  On Thu, 12 Jan 2012 06:03:16 PM Klaus Thoeni wrote:
  Hi guys,
  
  as discussed with Bruno in Barcelona I need different non-viscous
  damping coefficients for different materials. I introduced this
  capability by adding a variable damping to the base class material
  which is initialised with NaN. The body class has a function
  getDampCoeff() and in
  NewtonIntegrator I use this function in order to change the damping
  coefficients. When running some examples it seems that everything works
  fine. However, I just run 'yade --test' and it gives me a seg fault:
  
  testVelocity (yade.TestSimpleClump)
  Clump: velocities of member assigned by NewtonIntegrator ...
  Segmentation fault
  
  I think I now where the problem is. In NewtonIntegrator I call something
  like:
  
  if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();
  
  where getDampCoeff() is defined in body.hpp as:
  
  Real getDampCoeff() { return material-damping; };
  
  I think the test doesn't have a material and therefore I get the seg
  fault. Right? How can we fix this so that I can commit the code?
  
  Klaus
  
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Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Klaus Thoeni

Hi Anton,

actually it is the third body and it's a clump (isClump=True). Clumps should 
have a material too, shouldn't they?

Klaus

On Thu, 19 Jan 2012 06:31:09 PM Anton Gladky wrote:
   Real getDampCoeff() { return material-damping; };
 
 Can you check here a material existence?
 
 Anton
 
 On Thu, Jan 19, 2012 at 8:14 AM, Klaus Thoeni klaus.tho...@gmail.com 
wrote:
  Hi guys,
  
  can anyone help me on this?
  
  Klaus
  
  On Thu, 12 Jan 2012 06:03:16 PM Klaus Thoeni wrote:
  Hi guys,
  
  as discussed with Bruno in Barcelona I need different non-viscous
  damping coefficients for different materials. I introduced this
  capability by adding a variable damping to the base class material
  which is initialised with NaN. The body class has a function
  getDampCoeff() and in
  NewtonIntegrator I use this function in order to change the damping
  coefficients. When running some examples it seems that everything works
  fine. However, I just run 'yade --test' and it gives me a seg fault:
  
  testVelocity (yade.TestSimpleClump)
  Clump: velocities of member assigned by NewtonIntegrator ...
  Segmentation fault
  
  I think I now where the problem is. In NewtonIntegrator I call something
  like:
  
  if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();
  
  where getDampCoeff() is defined in body.hpp as:
  
  Real getDampCoeff() { return material-damping; };
  
  I think the test doesn't have a material and therefore I get the seg
  fault. Right? How can we fix this so that I can commit the code?
  
  Klaus
  
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Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Anton Gladky

Hmm, good question.
Maybe not. They consist of real spheres and those spheres should
have a material, I think.

Anton



On Thu, Jan 19, 2012 at 11:35 AM, Klaus Thoeni klaus.tho...@gmail.com wrote:
 Hi Anton,

 actually it is the third body and it's a clump (isClump=True). Clumps should
 have a material too, shouldn't they?

 Klaus

 On Thu, 19 Jan 2012 06:31:09 PM Anton Gladky wrote:
   Real getDampCoeff() { return material-damping; };

 Can you check here a material existence?

 Anton

 On Thu, Jan 19, 2012 at 8:14 AM, Klaus Thoeni klaus.tho...@gmail.com
 wrote:
  Hi guys,
 
  can anyone help me on this?
 
  Klaus
 
  On Thu, 12 Jan 2012 06:03:16 PM Klaus Thoeni wrote:
  Hi guys,
 
  as discussed with Bruno in Barcelona I need different non-viscous
  damping coefficients for different materials. I introduced this
  capability by adding a variable damping to the base class material
  which is initialised with NaN. The body class has a function
  getDampCoeff() and in
  NewtonIntegrator I use this function in order to change the damping
  coefficients. When running some examples it seems that everything works
  fine. However, I just run 'yade --test' and it gives me a seg fault:
 
  testVelocity (yade.TestSimpleClump)
  Clump: velocities of member assigned by NewtonIntegrator ...
  Segmentation fault
 
  I think I now where the problem is. In NewtonIntegrator I call something
  like:
 
  if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();
 
  where getDampCoeff() is defined in body.hpp as:
 
  Real getDampCoeff() { return material-damping; };
 
  I think the test doesn't have a material and therefore I get the seg
  fault. Right? How can we fix this so that I can commit the code?
 
  Klaus
 
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Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Klaus Thoeni

I just creeated a clump in a real simulation , and indeed, material gives 
'None'. So clumps have no material. Anyone knows why? Makes no sense to me.

Klaus

On Thu, 19 Jan 2012 09:51:38 PM Anton Gladky wrote:
 Hmm, good question.
 Maybe not. They consist of real spheres and those spheres should
 have a material, I think.
 
 Anton
 
 On Thu, Jan 19, 2012 at 11:35 AM, Klaus Thoeni klaus.tho...@gmail.com 
wrote:
  Hi Anton,
  
  actually it is the third body and it's a clump (isClump=True). Clumps
  should have a material too, shouldn't they?
  
  Klaus
  
  On Thu, 19 Jan 2012 06:31:09 PM Anton Gladky wrote:
Real getDampCoeff() { return material-damping; };
  
  Can you check here a material existence?
  
  Anton
  
  On Thu, Jan 19, 2012 at 8:14 AM, Klaus Thoeni klaus.tho...@gmail.com
  
  wrote:
   Hi guys,
   
   can anyone help me on this?
   
   Klaus
   
   On Thu, 12 Jan 2012 06:03:16 PM Klaus Thoeni wrote:
   Hi guys,
   
   as discussed with Bruno in Barcelona I need different non-viscous
   damping coefficients for different materials. I introduced this
   capability by adding a variable damping to the base class material
   which is initialised with NaN. The body class has a function
   getDampCoeff() and in
   NewtonIntegrator I use this function in order to change the damping
   coefficients. When running some examples it seems that everything
   works fine. However, I just run 'yade --test' and it gives me a seg
   fault:
   
   testVelocity (yade.TestSimpleClump)
   Clump: velocities of member assigned by NewtonIntegrator ...
   Segmentation fault
   
   I think I now where the problem is. In NewtonIntegrator I call
   something like:
   
   if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();
   
   where getDampCoeff() is defined in body.hpp as:
   
   Real getDampCoeff() { return material-damping; };
   
   I think the test doesn't have a material and therefore I get the seg
   fault. Right? How can we fix this so that I can commit the code?
   
   Klaus
   
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Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Klaus Thoeni

Solved the problem by checking if it is a clump:

Real getDampCoeff() { return (!Body::isClump) ? material-damping : NaN; };

However, I think we still have to sort out why clumps don't have a material!

I will commit the code, it might be useful to have different non-viscous 
damping coefficients, or what do you think?

Klaus

On Thu, 19 Jan 2012 09:51:38 PM Anton Gladky wrote:
 Hmm, good question.
 Maybe not. They consist of real spheres and those spheres should
 have a material, I think.
 
 Anton
 
 On Thu, Jan 19, 2012 at 11:35 AM, Klaus Thoeni klaus.tho...@gmail.com 
wrote:
  Hi Anton,
  
  actually it is the third body and it's a clump (isClump=True). Clumps
  should have a material too, shouldn't they?
  
  Klaus
  
  On Thu, 19 Jan 2012 06:31:09 PM Anton Gladky wrote:
Real getDampCoeff() { return material-damping; };
  
  Can you check here a material existence?
  
  Anton
  
  On Thu, Jan 19, 2012 at 8:14 AM, Klaus Thoeni klaus.tho...@gmail.com
  
  wrote:
   Hi guys,
   
   can anyone help me on this?
   
   Klaus
   
   On Thu, 12 Jan 2012 06:03:16 PM Klaus Thoeni wrote:
   Hi guys,
   
   as discussed with Bruno in Barcelona I need different non-viscous
   damping coefficients for different materials. I introduced this
   capability by adding a variable damping to the base class material
   which is initialised with NaN. The body class has a function
   getDampCoeff() and in
   NewtonIntegrator I use this function in order to change the damping
   coefficients. When running some examples it seems that everything
   works fine. However, I just run 'yade --test' and it gives me a seg
   fault:
   
   testVelocity (yade.TestSimpleClump)
   Clump: velocities of member assigned by NewtonIntegrator ...
   Segmentation fault
   
   I think I now where the problem is. In NewtonIntegrator I call
   something like:
   
   if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();
   
   where getDampCoeff() is defined in body.hpp as:
   
   Real getDampCoeff() { return material-damping; };
   
   I think the test doesn't have a material and therefore I get the seg
   fault. Right? How can we fix this so that I can commit the code?
   
   Klaus
   
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Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Anton Gladky

Could you, please, attach a diff first?
Thanks

Anton



On Thu, Jan 19, 2012 at 1:03 PM, Klaus Thoeni klaus.tho...@gmail.com wrote:
 Solved the problem by checking if it is a clump:

 Real getDampCoeff() { return (!Body::isClump) ? material-damping : NaN; };

 However, I think we still have to sort out why clumps don't have a material!

 I will commit the code, it might be useful to have different non-viscous
 damping coefficients, or what do you think?

 Klaus

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Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Klaus Thoeni

Here is the diff, effected classes Body, Material, NewtonIntegrator. Let me 
know 
if you are happy!

=== modified file core/Body.hpp
--- core/Body.hpp   2010-12-22 10:55:23 +
+++ core/Body.hpp   2012-01-19 11:40:50 +
@@ -68,6 +68,8 @@
 
int getGroupMask() {return groupMask; };
bool maskOk(int mask){return (mask==0 || (groupMaskmask));}
+   
+   Real getDampCoeff() { return (!Body::isClump) ? 
material-damping : NaN; 
};
 
// only BodyContainer can set the id of a body
friend class BodyContainer;

=== modified file core/Material.hpp
--- core/Material.hpp   2010-11-07 11:46:20 +
+++ core/Material.hpp   2012-01-12 05:50:12 +
@@ -39,7 +39,8 @@
YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Material,Serializable,Material 
properties of a :yref:`bodyBody`.,
((int,id,((void)not shared,-1),Attr::readonly,Numeric id of 
this 
material; is non-negative only if this Material is shared (i.e. in 
O.materials), -1 otherwise. This value is set automatically when the material 
is inserted to the simulation via 
:yref:`O.materials.appendMaterialContainer.append`. (This id was necessary 
since before boost::serialization was used, shared pointers were not tracked 
properly; it might disappear in the future)))
((string,label,,,Textual identifier for this material; can be 
used for 
shared materials lookup in :yref:`MaterialContainer`.))
-   ((Real,density,1000,,Density of the material [kg/m³])),
+   ((Real,density,1000,,Density of the material [kg/m³]))
+   ((Real,damping,NaN,,Local damping coefficient associated with 
the 
material [-]. If this value is given :yref:`Newtonintegrator` uses this value 
instead of :yref:`dampingNewtonIntegrator.damping` and it allows to use 
different damping coefficients for different materials.)),
/* ctor */,
/*py*/
.def(newAssocState,Material::newAssocState,Return new 
:yref:`State` 
instance, which is associated with this :yref:`Material`. Some materials have 
special requirement on :yref:`Body::state` type and calling this function when 
the body is created will ensure that they match. (This is done automatically 
if you use utils.sphere, … functions from python).)

=== modified file pkg/dem/NewtonIntegrator.cpp
--- pkg/dem/NewtonIntegrator.cpp2011-11-30 17:39:33 +
+++ pkg/dem/NewtonIntegrator.cpp2012-01-19 11:56:41 +
@@ -11,17 +11,18 @@
 #includeyade/pkg/dem/Clump.hpp
 #includeyade/pkg/common/VelocityBins.hpp
 #includeyade/lib/base/Math.hpp
+#include ../../lib/base/Logging.hpp
 
 YADE_PLUGIN((NewtonIntegrator));
 CREATE_LOGGER(NewtonIntegrator);
 
 // 1st order numerical damping
-void NewtonIntegrator::cundallDamp1st(Vector3r force, const Vector3r vel){
-   for(int i=0; i3; i++) force[i]*=1-damping*Mathr::Sign(force[i]*vel[i]);
+void NewtonIntegrator::cundallDamp1st(Vector3r force, const Vector3r vel, 
const Real dampcoeff){
+   for(int i=0; i3; i++) 
force[i]*=1-dampcoeff*Mathr::Sign(force[i]*vel[i]);
 }
 // 2nd order numerical damping
-void NewtonIntegrator::cundallDamp2nd(const Real dt, const Vector3r force, 
const Vector3r vel, Vector3r accel){
-   for(int i=0; i3; i++) accel[i]*= 1 - damping*Mathr::Sign ( 
force[i]*(vel[i] + 0.5*dt*accel[i]) );
+void NewtonIntegrator::cundallDamp2nd(const Real dt, const Vector3r force, 
const Vector3r vel, Vector3r accel, const Real dampcoeff){
+   for(int i=0; i3; i++) accel[i]*= 1 - dampcoeff*Mathr::Sign ( 
force[i]*(vel[i] + 0.5*dt*accel[i]) );
 }
 
 Vector3r NewtonIntegrator::computeAccel(const Vector3r force, const Real 
mass, int blockedDOFs){
@@ -39,11 +40,14 @@
 
 void NewtonIntegrator::updateEnergy(const shared_ptrBody b, const State* 
state, const Vector3r fluctVel, const Vector3r f, const Vector3r m){
assert(b-isStandalone() || b-isClump());
-   // always positive dissipation, by-component: |F_i|*|v_i|*damping*dt (|
T_i|*|ω_i|*damping*dt for rotations)
-   if(damping!=0.){
-   scene-energy-
add(fluctVel.cwise().abs().dot(f.cwise().abs())*damping*scene-
dt,nonviscDamp,nonviscDampIx,/*non-incremental*/false);
+   // check which damping coefficient to use
+   Real dampcoeff=damping;
+   if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();
+   // always positive dissipation, by-component: |F_i|*|v_i|*dampcoeff*dt 
(|
T_i|*|ω_i|*dampcoeff*dt for rotations)
+   if(dampcoeff!=0.){
+   scene-energy-
add(fluctVel.cwise().abs().dot(f.cwise().abs())*dampcoeff*scene-
dt,nonviscDamp,nonviscDampIx,/*non-incremental*/false);
// when the aspherical integrator is used, torque is damped 
instead of 
ang acceleration; this code is only approximate
-   scene-energy-add(state-
angVel.cwise().abs().dot(m.cwise().abs())*damping*scene-
dt,nonviscDamp,nonviscDampIx,false);
+   scene-energy-add(state-

Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Bruno Chareyre

Hi Klaus,

1/ I don't really understand what you did and what the problem is. I
know what density scaling is (what we discussed in Barcelona iirc), but
it is not a form of damping and doesn't need anything new in materials.
Instead, it uses the per-body timestep.
2/ In order to be sure where the crash is, you should test in debug mode.

Bruno

On 19/01/12 08:14, Klaus Thoeni wrote:
 Hi guys,

 can anyone help me on this?

 Klaus

 On Thu, 12 Jan 2012 06:03:16 PM Klaus Thoeni wrote:
 Hi guys,

 as discussed with Bruno in Barcelona I need different non-viscous damping
 coefficients for different materials. I introduced this capability by
 adding a variable damping to the base class material which is initialised
 with NaN. The body class has a function getDampCoeff() and in
 NewtonIntegrator I use this function in order to change the damping
 coefficients. When running some examples it seems that everything works
 fine. However, I just run 'yade --test' and it gives me a seg fault:

 testVelocity (yade.TestSimpleClump)
 Clump: velocities of member assigned by NewtonIntegrator ... Segmentation
 fault

 I think I now where the problem is. In NewtonIntegrator I call something
 like:

 if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();

 where getDampCoeff() is defined in body.hpp as:

 Real getDampCoeff() { return material-damping; };

 I think the test doesn't have a material and therefore I get the seg fault.
 Right? How can we fix this so that I can commit the code?

 Klaus
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-- 
___
Bruno Chareyre
Associate Professor
ENSE³ - Grenoble INP
11, rue des Mathématiques
BP 46
38402 St Martin d'Hères, France
Tél : +33 4 56 52 86 21
Fax : +33 4 76 82 70 43



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Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Bruno Chareyre

(sorry for previous message, I didnt see the full discussion)
As Anton says, a clump is a collection of bodies (not only spheres), and
each of them have a material. At the clump's scale, material properties
would be useless.

Bruno


On 19/01/12 11:56, Klaus Thoeni wrote:
 I just creeated a clump in a real simulation , and indeed, material gives 
 'None'. So clumps have no material. Anyone knows why? Makes no sense to me.

 Klaus

 On Thu, 19 Jan 2012 09:51:38 PM Anton Gladky wrote:
 Hmm, good question.
 Maybe not. They consist of real spheres and those spheres should
 have a material, I think.

 Anton

 On Thu, Jan 19, 2012 at 11:35 AM, Klaus Thoeni klaus.tho...@gmail.com 
 wrote:
 Hi Anton,

 actually it is the third body and it's a clump (isClump=True). Clumps
 should have a material too, shouldn't they?

 Klaus

 On Thu, 19 Jan 2012 06:31:09 PM Anton Gladky wrote:
   Real getDampCoeff() { return material-damping; };

 Can you check here a material existence?

 Anton

 On Thu, Jan 19, 2012 at 8:14 AM, Klaus Thoeni klaus.tho...@gmail.com
 wrote:
 Hi guys,

 can anyone help me on this?

 Klaus

 On Thu, 12 Jan 2012 06:03:16 PM Klaus Thoeni wrote:
 Hi guys,

 as discussed with Bruno in Barcelona I need different non-viscous
 damping coefficients for different materials. I introduced this
 capability by adding a variable damping to the base class material
 which is initialised with NaN. The body class has a function
 getDampCoeff() and in
 NewtonIntegrator I use this function in order to change the damping
 coefficients. When running some examples it seems that everything
 works fine. However, I just run 'yade --test' and it gives me a seg
 fault:

 testVelocity (yade.TestSimpleClump)
 Clump: velocities of member assigned by NewtonIntegrator ...
 Segmentation fault

 I think I now where the problem is. In NewtonIntegrator I call
 something like:

 if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();

 where getDampCoeff() is defined in body.hpp as:

 Real getDampCoeff() { return material-damping; };

 I think the test doesn't have a material and therefore I get the seg
 fault. Right? How can we fix this so that I can commit the code?

 Klaus
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Bruno Chareyre
Associate Professor
ENSE³ - Grenoble INP
11, rue des Mathématiques
BP 46
38402 St Martin d'Hères, France
Tél : +33 4 56 52 86 21
Fax : +33 4 76 82 70 43



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Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Bruno Chareyre

Still not good Klaus sorry. Bodies without material are allowed. Your
change should not crash yade in that case.

 Solved the problem by checking if it is a clump:


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Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Anton Gladky

One note:

if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();

I think it is not optimal to check (if(!isnan(b-getDampCoeff( on
_every_ interaction on _each_ step (performance!!!).
As I understand, you do not use damping-variable of Newtonintegrator
at all, so just set it to -1 and use it as flag.
So you will check it 1 time per step.

But it needs to be documented.

I dont see any large problems with this commit. If you really need it,
you can do it after fixing this issue.

Anton



On Thu, Jan 19, 2012 at 1:48 PM, Klaus Thoeni klaus.tho...@gmail.com wrote:
 Here is the diff, effected classes Body, Material, NewtonIntegrator. Let me 
 know
 if you are happy!

 === modified file core/Body.hpp
 --- core/Body.hpp       2010-12-22 10:55:23 +
 +++ core/Body.hpp       2012-01-19 11:40:50 +
 @@ -68,6 +68,8 @@

                int getGroupMask() {return groupMask; };
                bool maskOk(int mask){return (mask==0 || (groupMaskmask));}
 +
 +               Real getDampCoeff() { return (!Body::isClump) ? 
 material-damping : NaN;
 };

                // only BodyContainer can set the id of a body
                friend class BodyContainer;

 === modified file core/Material.hpp
 --- core/Material.hpp   2010-11-07 11:46:20 +
 +++ core/Material.hpp   2012-01-12 05:50:12 +
 @@ -39,7 +39,8 @@
        YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Material,Serializable,Material
 properties of a :yref:`bodyBody`.,
                ((int,id,((void)not shared,-1),Attr::readonly,Numeric id of 
 this
 material; is non-negative only if this Material is shared (i.e. in
 O.materials), -1 otherwise. This value is set automatically when the material
 is inserted to the simulation via
 :yref:`O.materials.appendMaterialContainer.append`. (This id was necessary
 since before boost::serialization was used, shared pointers were not tracked
 properly; it might disappear in the future)))
                ((string,label,,,Textual identifier for this material; can be 
 used for
 shared materials lookup in :yref:`MaterialContainer`.))
 -               ((Real,density,1000,,Density of the material [kg/m³])),
 +               ((Real,density,1000,,Density of the material [kg/m³]))
 +               ((Real,damping,NaN,,Local damping coefficient associated 
 with the
 material [-]. If this value is given :yref:`Newtonintegrator` uses this value
 instead of :yref:`dampingNewtonIntegrator.damping` and it allows to use
 different damping coefficients for different materials.)),
                /* ctor */,
                /*py*/
                .def(newAssocState,Material::newAssocState,Return new 
 :yref:`State`
 instance, which is associated with this :yref:`Material`. Some materials have
 special requirement on :yref:`Body::state` type and calling this function when
 the body is created will ensure that they match. (This is done automatically
 if you use utils.sphere, … functions from python).)

 === modified file pkg/dem/NewtonIntegrator.cpp
 --- pkg/dem/NewtonIntegrator.cpp        2011-11-30 17:39:33 +
 +++ pkg/dem/NewtonIntegrator.cpp        2012-01-19 11:56:41 +
 @@ -11,17 +11,18 @@
  #includeyade/pkg/dem/Clump.hpp
  #includeyade/pkg/common/VelocityBins.hpp
  #includeyade/lib/base/Math.hpp
 +#include ../../lib/base/Logging.hpp

  YADE_PLUGIN((NewtonIntegrator));
  CREATE_LOGGER(NewtonIntegrator);

  // 1st order numerical damping
 -void NewtonIntegrator::cundallDamp1st(Vector3r force, const Vector3r vel){
 -       for(int i=0; i3; i++) 
 force[i]*=1-damping*Mathr::Sign(force[i]*vel[i]);
 +void NewtonIntegrator::cundallDamp1st(Vector3r force, const Vector3r vel,
 const Real dampcoeff){
 +       for(int i=0; i3; i++) 
 force[i]*=1-dampcoeff*Mathr::Sign(force[i]*vel[i]);
  }
  // 2nd order numerical damping
 -void NewtonIntegrator::cundallDamp2nd(const Real dt, const Vector3r force,
 const Vector3r vel, Vector3r accel){
 -       for(int i=0; i3; i++) accel[i]*= 1 - damping*Mathr::Sign (
 force[i]*(vel[i] + 0.5*dt*accel[i]) );
 +void NewtonIntegrator::cundallDamp2nd(const Real dt, const Vector3r force,
 const Vector3r vel, Vector3r accel, const Real dampcoeff){
 +       for(int i=0; i3; i++) accel[i]*= 1 - dampcoeff*Mathr::Sign (
 force[i]*(vel[i] + 0.5*dt*accel[i]) );
  }

  Vector3r NewtonIntegrator::computeAccel(const Vector3r force, const Real
 mass, int blockedDOFs){
 @@ -39,11 +40,14 @@

  void NewtonIntegrator::updateEnergy(const shared_ptrBody b, const State*
 state, const Vector3r fluctVel, const Vector3r f, const Vector3r m){
        assert(b-isStandalone() || b-isClump());
 -       // always positive dissipation, by-component: |F_i|*|v_i|*damping*dt 
 (|
 T_i|*|ω_i|*damping*dt for rotations)
 -       if(damping!=0.){
 -               scene-energy-
add(fluctVel.cwise().abs().dot(f.cwise().abs())*damping*scene-
dt,nonviscDamp,nonviscDampIx,/*non-incremental*/false);
 +       // check which damping coefficient to use
 +       Real dampcoeff=damping;
 +       if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();

Re: [Yade-dev] : Add damping coefficient to material

2012-01-19 Thread Bruno Chareyre

Klaus,
If what you want is to increase the timestep (because your steel-net
induces very small dt, right?), this change will not work. You need to
modify density in the good place in Newton, not damping. It can be done
by adding dscale parameter in the material class (hence no need to check
if it exists), which would be 1 by default, hence no need to check if it
is NaN.
isnan is not in C++ standard, by the way. I know it is used in many
places but we should avoid it if possible. I'm also not sure of the cost
of this function, it may be more expensive than comparing two doubles.

Bruno


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Re: [Yade-dev] : Add damping coefficient to material

2012-01-18 Thread Klaus Thoeni

Hi guys,

can anyone help me on this?

Klaus

On Thu, 12 Jan 2012 06:03:16 PM Klaus Thoeni wrote:
 Hi guys,
 
 as discussed with Bruno in Barcelona I need different non-viscous damping
 coefficients for different materials. I introduced this capability by
 adding a variable damping to the base class material which is initialised
 with NaN. The body class has a function getDampCoeff() and in
 NewtonIntegrator I use this function in order to change the damping
 coefficients. When running some examples it seems that everything works
 fine. However, I just run 'yade --test' and it gives me a seg fault:
 
 testVelocity (yade.TestSimpleClump)
 Clump: velocities of member assigned by NewtonIntegrator ... Segmentation
 fault
 
 I think I now where the problem is. In NewtonIntegrator I call something
 like:
 
 if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();
 
 where getDampCoeff() is defined in body.hpp as:
 
 Real getDampCoeff() { return material-damping; };
 
 I think the test doesn't have a material and therefore I get the seg fault.
 Right? How can we fix this so that I can commit the code?
 
 Klaus

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Re: [Yade-dev] : Add damping coefficient to material

2012-01-18 Thread Anton Gladky

  Real getDampCoeff() { return material-damping; };

Can you check here a material existence?

Anton



On Thu, Jan 19, 2012 at 8:14 AM, Klaus Thoeni klaus.tho...@gmail.com wrote:
 Hi guys,

 can anyone help me on this?

 Klaus

 On Thu, 12 Jan 2012 06:03:16 PM Klaus Thoeni wrote:
 Hi guys,

 as discussed with Bruno in Barcelona I need different non-viscous damping
 coefficients for different materials. I introduced this capability by
 adding a variable damping to the base class material which is initialised
 with NaN. The body class has a function getDampCoeff() and in
 NewtonIntegrator I use this function in order to change the damping
 coefficients. When running some examples it seems that everything works
 fine. However, I just run 'yade --test' and it gives me a seg fault:

 testVelocity (yade.TestSimpleClump)
 Clump: velocities of member assigned by NewtonIntegrator ... Segmentation
 fault

 I think I now where the problem is. In NewtonIntegrator I call something
 like:

 if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();

 where getDampCoeff() is defined in body.hpp as:

 Real getDampCoeff() { return material-damping; };

 I think the test doesn't have a material and therefore I get the seg fault.
 Right? How can we fix this so that I can commit the code?

 Klaus

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[Yade-dev] : Add damping coefficient to material

2012-01-11 Thread Klaus Thoeni

Hi guys,

as discussed with Bruno in Barcelona I need different non-viscous damping 
coefficients for different materials. I introduced this capability by adding a 
variable damping to the base class material which is initialised with NaN. The 
body class has a function getDampCoeff() and in NewtonIntegrator I use this 
function in order to change the damping coefficients. When running some 
examples 
it seems that everything works fine. However, I just run 'yade --test' and it 
gives me a seg fault:

testVelocity (yade.TestSimpleClump)
Clump: velocities of member assigned by NewtonIntegrator ... Segmentation 
fault

I think I now where the problem is. In NewtonIntegrator I call something like:

if(!isnan(b-getDampCoeff())) dampcoeff=b-getDampCoeff();

where getDampCoeff() is defined in body.hpp as:

Real getDampCoeff() { return material-damping; };

I think the test doesn't have a material and therefore I get the seg fault. 
Right? How can we fix this so that I can commit the code?

Klaus

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Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

Re: [Yade-dev] : Add damping coefficient to material

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[Yade-dev] : Add damping coefficient to material

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