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Message #12501
[Branch ~yade-pkg/yade/git-trunk] Rev 3771: Implement deformable elements
------------------------------------------------------------
revno: 3771
author: Burak Er <burak.er@xxxxxxxxxx>
committer: Anton Gladky <gladky.anton@xxxxxxxxx>
timestamp: Thu 2016-01-07 18:49:32 +0100
message:
Implement deformable elements
The deformable elements are the finite-discrete elements that are
connected together with interaction elements. The interaction element
hold discrete finite elements together with applying fictitious forces
if they separate from each other. With this approach their connectivity
is provided as in the case of Finite element method.
https://www.researchgate.net/publication/286870976_Wave_Propagation_in_Galerkin_Based_Discrete_Element_Particles
added:
examples/deformableelem/
examples/deformableelem/Minimal.py
examples/deformableelem/MinimalTensileTest.py
examples/deformableelem/ReadMe
examples/deformableelem/main.py
examples/deformableelem/model.geo
examples/deformableelem/model.msh
examples/deformableelem/model.stl
examples/deformableelem/testDeformableBodies.py
examples/deformableelem/testDeformableBodies_pressure.py
pkg/dem/deformablecohesive/
pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.cpp
pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.hpp
pkg/dem/deformablecohesive/Bo1_Node_Aabb.cpp
pkg/dem/deformablecohesive/Bo1_Node_Aabb.hpp
pkg/dem/deformablecohesive/CohesiveMat.cpp
pkg/dem/deformablecohesive/CohesiveMat.hpp
pkg/dem/deformablecohesive/DeformableCohesiveElement.cpp
pkg/dem/deformablecohesive/DeformableCohesiveElement.hpp
pkg/dem/deformablecohesive/DeformableElement.cpp
pkg/dem/deformablecohesive/DeformableElement.hpp
pkg/dem/deformablecohesive/FEInternalForceDispatchers.cpp
pkg/dem/deformablecohesive/FEInternalForceDispatchers.hpp
pkg/dem/deformablecohesive/FEInternalForceEngine.cpp
pkg/dem/deformablecohesive/FEInternalForceEngine.hpp
pkg/dem/deformablecohesive/Gl1_DeformableElement.cpp
pkg/dem/deformablecohesive/Gl1_DeformableElement.hpp
pkg/dem/deformablecohesive/Gl1_Node.cpp
pkg/dem/deformablecohesive/Gl1_Node.hpp
pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.cpp
pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.hpp
pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.cpp
pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.hpp
pkg/dem/deformablecohesive/Lin4NodeTetra.cpp
pkg/dem/deformablecohesive/Lin4NodeTetra.hpp
pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.cpp
pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.hpp
pkg/dem/deformablecohesive/LinElastMat.cpp
pkg/dem/deformablecohesive/LinElastMat.hpp
pkg/dem/deformablecohesive/Node.cpp
pkg/dem/deformablecohesive/Node.hpp
py/deformableelementsutils.py
modified:
core/Shape.hpp
py/utils.py
py/ymport.py
--
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=== modified file 'core/Shape.hpp'
--- core/Shape.hpp 2014-10-15 06:44:01 +0000
+++ core/Shape.hpp 2016-01-07 17:49:32 +0000
@@ -16,12 +16,16 @@
class BoundFunctor;
+class InternalForceFunctor;
+
class Shape: public Serializable, public Indexable {
public:
- ~Shape() {}; // vtable
+ virtual ~Shape() {}; // vtable
#ifdef BV_FUNCTOR_CACHE
shared_ptr<BoundFunctor> boundFunctor;
#endif
+ //! cache functor that are called for this type of DeformableElement. Used by FEInternalForceEngine
+ shared_ptr<InternalForceFunctor> internalforcefunctor;
YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Shape,Serializable,"Geometry of a body",
((Vector3r,color,Vector3r(1,1,1),,"Color for rendering (normalized RGB)."))
=== added directory 'examples/deformableelem'
=== added file 'examples/deformableelem/Minimal.py'
--- examples/deformableelem/Minimal.py 1970-01-01 00:00:00 +0000
+++ examples/deformableelem/Minimal.py 2016-01-07 17:49:32 +0000
@@ -0,0 +1,98 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# Created by Burak ER
+from yade.deformableelementsutils import *;
+
+O=Omega()
+
+## Create deformable elements internal materials and interaction element material
+
+mat=LinIsoRayleighDampElastMat(label='aluminiummaterial');
+
+intermat=LinCohesiveStiffPropDampElastMat(label='intermat')
+
+intermat.youngmodulus=70e11;
+
+mat.density=2700;
+
+mat.youngmodulus=70e9
+
+O.materials.append(intermat)
+
+O.materials.append(mat)
+
+## Generate deformable element mesh from GMSH2 format
+
+nodesofelement1=[[0, 0 ,0],[0, 1, 0],[1 ,0 ,0],[0, 0 ,1]]
+nodesofelement2=[[0, 0 ,0],[0, 1, 0],[1,0 ,0],[0, 0 ,-1]]
+
+
+noderadius=0.1*(0.75*tetrahedronvolume(nodesofelement1))**0.33333333;
+
+[elbody, nodebodies1]=tetrahedral_element(mat,nodesofelement1,Lin4NodeTetra,radius=noderadius)
+[elbody, nodebodies2]=tetrahedral_element(mat,nodesofelement2,Lin4NodeTetra,radius=noderadius)
+nodebodies1[3].state.pos+=Vector3(0,0,0.01);
+
+
+interfaceelementpairs=[];
+interfaceelementpairs.append([nodebodies1[0], nodebodies2[0]]);
+interfaceelementpairs.append([nodebodies1[1], nodebodies2[1]]);
+interfaceelementpairs.append([nodebodies1[2], nodebodies2[2]]);
+
+[elbody, nodebodies]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement);
+
+
+
+#mesh=tetrahedral_mesh_generator('model.msh',Lin4NodeTetra,'aluminiummaterial',Lin4NodeTetra_Lin4NodeTetra_InteractionElement,'intermat')
+
+## Define the body boundary force
+
+# x position limits of bodies that are subject to the force
+force_tail_body_lowerlimit=-1.01;
+
+force_tail_body_upperlimit=-0.9999;
+
+# Angular frequency of the force
+amplitude=100000;
+
+period=(1e-3)
+
+omega=2*pi/period;
+
+applicationperiod=period/2;
+
+## Define the fixed boundary
+
+# x position limits of bodies that are subject to the fixed boundary
+
+fixed_tail_body_lowerlimit=0.99;
+
+fixed_tail_body_upperlimit=1.01;
+
+
+
+# Time step determines the exiting period of the integrator since the integrator performs one step from current_time to current_time+dt; using many substeps for any value of dt; then stops.
+
+O.dt=1e-9;
+
+O.engines=[
+ ForceResetter(),
+ ## Apply internal force to the deformable elements and internal force of the interaction element
+ FEInternalForceEngine([If2_Lin4NodeTetra_LinIsoRayleighDampElast(),If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat()]),
+ NewtonIntegrator(damping=0,gravity=[0,0,0]),
+ #PyRunner(virtPeriod=1e-99,command='applyforcetoelements()'),
+ # ## Plotting data: adds plots after one step of the integrator engine
+ #PyRunner(virtPeriod=1e-99,command='addplot()')
+ ]
+
+from yade import plot
+
+plot.plots={'t':'vel','time':'pos','tm':'force'}
+plot.plot(subPlots=True)
+
+try:
+ from yade import qt
+ qt.View()
+ qt.Controller()
+except ImportError: pass
+
=== added file 'examples/deformableelem/MinimalTensileTest.py'
--- examples/deformableelem/MinimalTensileTest.py 1970-01-01 00:00:00 +0000
+++ examples/deformableelem/MinimalTensileTest.py 2016-01-07 17:49:32 +0000
@@ -0,0 +1,206 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# Created by Burak ER
+from yade.deformableelementsutils import *;
+
+O=Omega()
+
+pressure=70e7;# N/m^2
+wx=1;#m
+wy=1;#m
+wz=1;#m
+## Create deformable elements internal materials and interaction element material
+
+mat=LinIsoRayleighDampElastMat(label='aluminiummaterial');
+
+intermat=LinCohesiveStiffPropDampElastMat(label='intermat')
+
+intermat.youngmodulus=70e11;
+
+mat.density=2700;
+
+mat.beta=0.05;
+
+mat.alpha=0.05;
+
+mat.youngmodulus=70e9;
+
+O.materials.append(intermat)
+
+O.materials.append(mat)
+
+
+
+
+#create points of a cube with number of 8 points
+p0=Vector3([0, 0 ,0]);
+p1=Vector3([0, wy, 0]);
+p2=Vector3([wx ,0 ,0]);
+p3=Vector3([0, 0 ,wz]);
+p4=Vector3([0, wy, wz]);
+p5=Vector3([wx, wy, 0]);
+p6=Vector3([wx, 0 ,wz]);
+p7=Vector3([wx, wy ,wz]);
+
+nodesofelement1=[p0,p1,p2,p3];
+nodesofelement2=[p3,p4,p1,p7];
+nodesofelement3=[p2,p5,p1,p7];
+nodesofelement4=[p7,p2,p3,p6];
+nodesofelement5=[p1,p2,p3,p7];
+
+
+
+
+
+noderadius=0.1*(0.75*tetrahedronvolume(nodesofelement1))**0.33333333;
+
+[elbody1, nodebodies1]=tetrahedral_element(mat,nodesofelement1,Lin4NodeTetra,radius=noderadius)
+[elbody2, nodebodies2]=tetrahedral_element(mat,nodesofelement2,Lin4NodeTetra,radius=noderadius)
+[elbody3, nodebodies3]=tetrahedral_element(mat,nodesofelement3,Lin4NodeTetra,radius=noderadius)
+[elbody4, nodebodies4]=tetrahedral_element(mat,nodesofelement4,Lin4NodeTetra,radius=noderadius)
+[elbody5, nodebodies5]=tetrahedral_element(mat,nodesofelement5,Lin4NodeTetra,radius=noderadius)
+
+
+
+interfaceelementpairs=[];
+#interface of 1-5
+interfaceelementpairs.append([nodebodies1[1], nodebodies5[0]]);
+interfaceelementpairs.append([nodebodies1[2], nodebodies5[1]]);
+interfaceelementpairs.append([nodebodies1[3], nodebodies5[2]]);
+
+[elbodyinter, nodebodiesinter]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement);
+
+#interface of 2-5
+interfaceelementpairs=[];
+interfaceelementpairs.append([nodebodies2[0], nodebodies5[2]]);
+interfaceelementpairs.append([nodebodies2[2], nodebodies5[0]]);
+interfaceelementpairs.append([nodebodies2[3], nodebodies5[3]]);
+
+[elbodyinter, nodebodiesinter]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement);
+
+#interface of 3-5
+interfaceelementpairs=[];
+interfaceelementpairs.append([nodebodies3[0], nodebodies5[1]]);
+interfaceelementpairs.append([nodebodies3[2], nodebodies5[0]]);
+interfaceelementpairs.append([nodebodies3[3], nodebodies5[3]]);
+
+[elbodyinter, nodebodiesinter]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement);
+
+#interface of 3-5
+interfaceelementpairs=[];
+interfaceelementpairs.append([nodebodies3[0], nodebodies5[1]]);
+interfaceelementpairs.append([nodebodies3[2], nodebodies5[0]]);
+interfaceelementpairs.append([nodebodies3[3], nodebodies5[3]]);
+[elbodyinter, nodebodiesinter]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement);
+
+#interface of 4-5
+interfaceelementpairs=[];
+interfaceelementpairs.append([nodebodies4[0], nodebodies5[3]]);
+interfaceelementpairs.append([nodebodies4[1], nodebodies5[1]]);
+interfaceelementpairs.append([nodebodies4[2], nodebodies5[2]]);
+[elbodyinter, nodebodiesinter]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement);
+
+
+# Time step determines the exiting period of the integrator since the integrator performs one step from current_time to current_time+dt; using many substeps for any value of dt; then stops.
+initpos0=O.bodies[nodebodies1[0].id].state.pos;
+
+
+
+def applyforcetoelements():
+
+ pos0=O.bodies[nodebodies3[0].id].state.pos;
+ pos1=O.bodies[nodebodies3[1].id].state.pos;
+ pos2=O.bodies[nodebodies3[2].id].state.pos;
+ area1=0.5*((pos1-pos0).cross(pos2-pos0)).norm();
+
+
+ pos0=O.bodies[nodebodies1[0].id].state.pos;
+ pos1=O.bodies[nodebodies1[1].id].state.pos;
+ pos2=O.bodies[nodebodies1[2].id].state.pos;
+ area2=0.5*((pos1-pos0).cross(pos2-pos0)).norm();
+
+
+ Traction=area1*pressure;
+
+ O.forces.addF(nodebodies3[0].id,Vector3(0,0,-(0.3*Traction)));
+ O.forces.addF(nodebodies3[1].id,Vector3(0,0,-(0.3*Traction)));
+ O.forces.addF(nodebodies3[2].id,Vector3(0,0,-(0.3*Traction)));
+
+
+
+ Traction=area2*pressure;
+
+ O.forces.addF(nodebodies1[0].id,Vector3(0,0,-(0.3*Traction)));
+ O.forces.addF(nodebodies1[1].id,Vector3(0,0,-(0.3*Traction)));
+ O.forces.addF(nodebodies1[2].id,Vector3(0,0,-(0.3*Traction)));
+
+def fixboundryelements():
+
+ nodebodies1[3].state.blockedDOFs='xyzXYZ'
+ nodebodies2[0].state.blockedDOFs='xyzXYZ'
+ nodebodies2[1].state.blockedDOFs='xyzXYZ'
+ nodebodies2[3].state.blockedDOFs='xyzXYZ'
+ nodebodies3[3].state.blockedDOFs='xyzXYZ'
+ nodebodies4[0].state.blockedDOFs='xyzXYZ'
+ nodebodies4[2].state.blockedDOFs='xyzXYZ'
+ nodebodies4[3].state.blockedDOFs='xyzXYZ'
+ nodebodies5[2].state.blockedDOFs='xyzXYZ'
+ nodebodies5[3].state.blockedDOFs='xyzXYZ'
+
+
+fixboundryelements();
+
+
+def addplot():
+ vecpos=(O.bodies[nodebodies1[0].id].state.pos-initpos0)
+ plot.addData(displacement=abs(vecpos[2]),time=O.time)
+
+
+
+
+
+ ##integratoreng=RungeKuttaCashKarp54Integrator([
+ ## ForceResetter(),
+
+ ## Apply internal force to the deformable elements and internal force of the interaction element
+ ## FEInternalForceEngine([If2_Lin4NodeTetra_LinIsoRayleighDampElast(),If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat()]),
+
+ ## PyRunner(virtPeriod=1e-99,command='applyforcetoelements()'),
+
+
+ ##])
+
+ ##O.engines=[integratoreng,
+ ## PyRunner(iterPeriod=1,command='addplot()')
+ ##]
+
+ ##integratoreng.rel_err=1e-3;
+
+ ##integratoreng.abs_err=1e-3;
+O.engines=[ForceResetter(),
+ PyRunner(virtPeriod=1e-99,command='applyforcetoelements()'),
+ ## Apply internal force to the deformable elements and internal force of the interaction element
+
+ FEInternalForceEngine([If2_Lin4NodeTetra_LinIsoRayleighDampElast(),If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat()]),
+ NewtonIntegrator(damping=0,gravity=[0,0,0]),
+ PyRunner(virtPeriod=1e-99,command='addplot()'),
+
+];
+
+
+
+
+O.dt=1e-7;
+
+from yade import plot
+
+plot.plots={'time':'displacement'}
+
+plot.plot(subPlots=False)
+
+try:
+ from yade import qt
+ qt.View()
+ qt.Controller()
+except ImportError: pass
+
=== added file 'examples/deformableelem/ReadMe'
--- examples/deformableelem/ReadMe 1970-01-01 00:00:00 +0000
+++ examples/deformableelem/ReadMe 2016-01-07 17:49:32 +0000
@@ -0,0 +1,1 @@
+This folder includes the simulation files for the deformable elements.
=== added file 'examples/deformableelem/main.py'
--- examples/deformableelem/main.py 1970-01-01 00:00:00 +0000
+++ examples/deformableelem/main.py 2016-01-07 17:49:32 +0000
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# untitled.py
+#
+# Copyright 2014 Burak ER <burak@Newton>
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+# MA 02110-1301, USA.
+#
+#
+import sys
+
+from yadeimport import *
+
+
+
+def main():
+
+ execfile("testDeformableBodies_pressure.py");
+
+ return 0
+
+if __name__ == '__main__':
+ main()
+
=== added file 'examples/deformableelem/model.geo'
--- examples/deformableelem/model.geo 1970-01-01 00:00:00 +0000
+++ examples/deformableelem/model.geo 2016-01-07 17:49:32 +0000
@@ -0,0 +1,5 @@
+Merge "model.msh";
+Physical Volume(100002) = {100001};
+Physical Volume(100003) = {100001};
+Field[1] = Max;
+Field[1].FieldsList = {1, -3};
=== added file 'examples/deformableelem/model.msh'
--- examples/deformableelem/model.msh 1970-01-01 00:00:00 +0000
+++ examples/deformableelem/model.msh 2016-01-07 17:49:32 +0000
@@ -0,0 +1,2188 @@
+$MeshFormat
+2.000000 0 8
+$EndMeshFormat
+$Nodes
+391
+1 1.000000 -0.000000 0.100001
+2 1.000000 0.057628 0.081449
+3 1.000000 0.093943 0.033143
+4 1.000000 0.095747 -0.027197
+5 1.000000 0.057793 -0.081311
+6 1.000000 0.000213 -0.099978
+7 1.000000 -0.057462 -0.081583
+8 1.000000 -0.093881 -0.033347
+9 1.000000 -0.095809 0.026994
+10 1.000000 -0.061597 0.078191
+11 -1.000000 0.019509 0.098078
+12 -1.000000 -0.040630 0.091124
+13 -1.000000 -0.088702 0.045164
+14 -1.000000 -0.098583 -0.014392
+15 -1.000000 -0.072274 -0.068806
+16 -1.000000 -0.019297 -0.098100
+17 -1.000000 0.040819 -0.091026
+18 -1.000000 0.088058 -0.046370
+19 -1.000000 0.098604 0.014177
+20 -1.000000 0.072410 0.068640
+21 0.938054 0.024884 0.096449
+22 0.942040 0.099428 0.005807
+23 0.937511 -0.039138 0.091924
+24 0.938529 -0.099197 -0.008157
+25 0.937866 -0.085505 0.051146
+26 -0.935772 -0.009233 0.099090
+27 -0.935059 -0.098116 0.019135
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+61 0.802304 0.015762 0.098448
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+70 0.814331 -0.098360 -0.016659
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+75 -0.746826 -0.077739 0.062145
+76 0.755653 -0.085163 -0.051785
+77 -0.787922 0.096181 -0.025768
+78 0.813475 -0.089194 0.044245
+79 -0.736253 0.073409 -0.067424
+80 0.811367 -0.046396 0.088044
+81 0.879466 0.096680 -0.024119
+82 -0.750530 -0.015133 0.098509
+83 -0.770244 0.093506 0.034581
+84 -0.757482 0.046185 0.088156
+85 -0.760407 0.031490 -0.094445
+86 0.726801 0.044933 0.088826
+87 -0.746685 -0.075100 -0.065363
+88 0.808824 0.099272 0.007394
+89 0.745199 -0.021133 0.097586
+90 0.740502 0.093959 0.033089
+91 0.882076 0.063560 -0.076578
+92 0.822272 0.043508 -0.089586
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+$EndElements
=== added file 'examples/deformableelem/model.stl'
--- examples/deformableelem/model.stl 1970-01-01 00:00:00 +0000
+++ examples/deformableelem/model.stl 2016-01-07 17:49:32 +0000
@@ -0,0 +1,870 @@
+solid vcg
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+ outer loop
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+ endloop
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+ outer loop
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+ vertex 1.000000e+00 0.000000e+00 -9.999900e-02
+ vertex 1.000000e+00 1.950900e-02 -9.807800e-02
+ endloop
+ endfacet
+ facet normal -9.935726e-07 -9.799373e-02 9.951870e-01
+ outer loop
+ vertex 1.000000e+00 -0.000000e+00 1.000010e-01
+ vertex -1.000000e+00 -0.000000e+00 9.999900e-02
+ vertex -1.000000e+00 -1.950900e-02 9.807800e-02
+ endloop
+ endfacet
+ facet normal -5.004912e-07 -9.804380e-02 9.951821e-01
+ outer loop
+ vertex -1.000000e+00 -1.950900e-02 9.807800e-02
+ vertex 1.000000e+00 -1.950900e-02 9.807900e-02
+ vertex 1.000000e+00 -0.000000e+00 1.000010e-01
+ endloop
+ endfacet
+ facet normal -9.589596e-07 -2.902623e-01 9.569471e-01
+ outer loop
+ vertex -1.000000e+00 -3.826800e-02 9.238700e-02
+ vertex 1.000000e+00 -3.826800e-02 9.238900e-02
+ vertex 1.000000e+00 -1.950900e-02 9.807900e-02
+ endloop
+ endfacet
+ facet normal -4.812552e-07 -2.903089e-01 9.569330e-01
+ outer loop
+ vertex 1.000000e+00 -1.950900e-02 9.807900e-02
+ vertex -1.000000e+00 -1.950900e-02 9.807800e-02
+ vertex -1.000000e+00 -3.826800e-02 9.238700e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 -0.000000e+00
+ outer loop
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+ vertex -1.000000e+00 1.950900e-02 9.807800e-02
+ vertex -1.000000e+00 -1.950900e-02 9.807800e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 1.950900e-02 9.807800e-02
+ vertex -1.000000e+00 -3.826800e-02 9.238700e-02
+ vertex -1.000000e+00 -1.950900e-02 9.807800e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 -0.000000e+00
+ outer loop
+ vertex -1.000000e+00 1.950900e-02 9.807800e-02
+ vertex -1.000000e+00 3.826800e-02 9.238700e-02
+ vertex -1.000000e+00 -3.826800e-02 9.238700e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 3.826800e-02 9.238700e-02
+ vertex -1.000000e+00 -5.555700e-02 8.314600e-02
+ vertex -1.000000e+00 -3.826800e-02 9.238700e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 -0.000000e+00
+ outer loop
+ vertex -1.000000e+00 3.826800e-02 9.238700e-02
+ vertex -1.000000e+00 5.555700e-02 8.314600e-02
+ vertex -1.000000e+00 -5.555700e-02 8.314600e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 5.555700e-02 8.314600e-02
+ vertex -1.000000e+00 -7.071100e-02 7.071000e-02
+ vertex -1.000000e+00 -5.555700e-02 8.314600e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 -0.000000e+00
+ outer loop
+ vertex -1.000000e+00 5.555700e-02 8.314600e-02
+ vertex -1.000000e+00 7.071100e-02 7.071000e-02
+ vertex -1.000000e+00 -7.071100e-02 7.071000e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 7.071100e-02 7.071000e-02
+ vertex -1.000000e+00 -8.314700e-02 5.555600e-02
+ vertex -1.000000e+00 -7.071100e-02 7.071000e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 -0.000000e+00
+ outer loop
+ vertex -1.000000e+00 7.071100e-02 7.071000e-02
+ vertex -1.000000e+00 8.314700e-02 5.555600e-02
+ vertex -1.000000e+00 -8.314700e-02 5.555600e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 8.314700e-02 5.555600e-02
+ vertex -1.000000e+00 -9.238800e-02 3.826800e-02
+ vertex -1.000000e+00 -8.314700e-02 5.555600e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 -0.000000e+00
+ outer loop
+ vertex -1.000000e+00 8.314700e-02 5.555600e-02
+ vertex -1.000000e+00 9.238800e-02 3.826800e-02
+ vertex -1.000000e+00 -9.238800e-02 3.826800e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 9.238800e-02 3.826800e-02
+ vertex -1.000000e+00 -9.807900e-02 1.950800e-02
+ vertex -1.000000e+00 -9.238800e-02 3.826800e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 -0.000000e+00
+ outer loop
+ vertex -1.000000e+00 9.238800e-02 3.826800e-02
+ vertex -1.000000e+00 9.807900e-02 1.950800e-02
+ vertex -1.000000e+00 -9.807900e-02 1.950800e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 9.807900e-02 1.950800e-02
+ vertex -1.000000e+00 -1.000000e-01 -1.000000e-06
+ vertex -1.000000e+00 -9.807900e-02 1.950800e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 -0.000000e+00
+ outer loop
+ vertex -1.000000e+00 9.807900e-02 1.950800e-02
+ vertex -1.000000e+00 1.000000e-01 -1.000000e-06
+ vertex -1.000000e+00 -1.000000e-01 -1.000000e-06
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 1.000000e-01 -1.000000e-06
+ vertex -1.000000e+00 -9.807900e-02 -1.951000e-02
+ vertex -1.000000e+00 -1.000000e-01 -1.000000e-06
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 1.000000e-01 -1.000000e-06
+ vertex -1.000000e+00 9.807900e-02 -1.951000e-02
+ vertex -1.000000e+00 -9.807900e-02 -1.951000e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 9.807900e-02 -1.951000e-02
+ vertex -1.000000e+00 -9.238800e-02 -3.826900e-02
+ vertex -1.000000e+00 -9.807900e-02 -1.951000e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 9.807900e-02 -1.951000e-02
+ vertex -1.000000e+00 9.238800e-02 -3.826900e-02
+ vertex -1.000000e+00 -9.238800e-02 -3.826900e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 9.238800e-02 -3.826900e-02
+ vertex -1.000000e+00 -8.314700e-02 -5.555800e-02
+ vertex -1.000000e+00 -9.238800e-02 -3.826900e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 9.238800e-02 -3.826900e-02
+ vertex -1.000000e+00 8.314700e-02 -5.555800e-02
+ vertex -1.000000e+00 -8.314700e-02 -5.555800e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 8.314700e-02 -5.555800e-02
+ vertex -1.000000e+00 -7.071100e-02 -7.071100e-02
+ vertex -1.000000e+00 -8.314700e-02 -5.555800e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 8.314700e-02 -5.555800e-02
+ vertex -1.000000e+00 7.071100e-02 -7.071100e-02
+ vertex -1.000000e+00 -7.071100e-02 -7.071100e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 7.071100e-02 -7.071100e-02
+ vertex -1.000000e+00 -5.555700e-02 -8.314800e-02
+ vertex -1.000000e+00 -7.071100e-02 -7.071100e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 7.071100e-02 -7.071100e-02
+ vertex -1.000000e+00 5.555700e-02 -8.314800e-02
+ vertex -1.000000e+00 -5.555700e-02 -8.314800e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 5.555700e-02 -8.314800e-02
+ vertex -1.000000e+00 -3.826800e-02 -9.238900e-02
+ vertex -1.000000e+00 -5.555700e-02 -8.314800e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 5.555700e-02 -8.314800e-02
+ vertex -1.000000e+00 3.826800e-02 -9.238900e-02
+ vertex -1.000000e+00 -3.826800e-02 -9.238900e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 3.826800e-02 -9.238900e-02
+ vertex -1.000000e+00 -1.950900e-02 -9.807900e-02
+ vertex -1.000000e+00 -3.826800e-02 -9.238900e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 3.826800e-02 -9.238900e-02
+ vertex -1.000000e+00 1.950900e-02 -9.807900e-02
+ vertex -1.000000e+00 -1.950900e-02 -9.807900e-02
+ endloop
+ endfacet
+ facet normal -1.000000e+00 -0.000000e+00 0.000000e+00
+ outer loop
+ vertex -1.000000e+00 1.950900e-02 -9.807900e-02
+ vertex -1.000000e+00 0.000000e+00 -1.000010e-01
+ vertex -1.000000e+00 -1.950900e-02 -9.807900e-02
+ endloop
+ endfacet
+endsolid vcg
=== added file 'examples/deformableelem/testDeformableBodies.py'
--- examples/deformableelem/testDeformableBodies.py 1970-01-01 00:00:00 +0000
+++ examples/deformableelem/testDeformableBodies.py 2016-01-07 17:49:32 +0000
@@ -0,0 +1,151 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# Created by Burak ER
+from yade.deformableelementsutils import *;
+
+O=Omega()
+
+## Create deformable elements internal materials and interaction element material
+
+mat=LinIsoRayleighDampElastMat(label='aluminiummaterial');
+
+intermat=LinCohesiveStiffPropDampElastMat(label='intermat')
+
+intermat.youngmodulus=70e11;
+
+mat.density=2700;
+
+mat.youngmodulus=70e9
+
+O.materials.append(intermat)
+
+O.materials.append(mat)
+
+## Generate deformable element mesh from GMSH2 format
+
+mesh=tetrahedral_mesh_generator('model.msh',Lin4NodeTetra,'aluminiummaterial',Lin4NodeTetra_Lin4NodeTetra_InteractionElement,'intermat')
+
+## Define the body boundary force
+
+# x position limits of bodies that are subject to the force
+force_tail_body_lowerlimit=-1.01;
+
+force_tail_body_upperlimit=-0.9999;
+
+# Angular frequency of the force
+amplitude=1000;
+
+period=(1e-4)
+
+omega=2*pi/period;
+
+applicationperiod=period/2;
+
+## Define the fixed boundary
+
+# x position limits of bodies that are subject to the fixed boundary
+
+fixed_tail_body_lowerlimit=0.99;
+
+fixed_tail_body_upperlimit=1.01;
+
+
+def getinitialpos():
+ positions=[];
+ for body in O.bodies:
+ positions.append(body.state.pos)
+ return positions
+
+def getboundarybodies():
+ bdy=[];
+ for body in O.bodies:
+ if(body.shape.dispIndex==12):
+ if(body.state.pos[0]<fixed_tail_body_upperlimit):
+ if(body.state.pos[0]>fixed_tail_body_lowerlimit):
+ bdy.append(body.id)
+ return bdy
+
+def getforcebodies():
+ bdy=[];
+ for body in O.bodies:
+ if(body.shape.dispIndex==12):
+ if(body.state.pos[0]<force_tail_body_upperlimit):
+ if(body.state.pos[0]>force_tail_body_lowerlimit):
+ if(O.time<applicationperiod):
+ bdy.append(body.id)
+ return bdy
+
+initialpositions=getinitialpos();
+
+forcebodies=getforcebodies();
+
+boundarybodies=getboundarybodies();
+
+
+## definition of functions
+def fixboundaryelements():
+ for i in boundarybodies:
+ O.forces.addF(i,-O.forces.f(i))
+ O.forces.addT(i,-O.forces.m(i))
+
+def applyforcetoelements():
+ for i in forcebodies:
+ if(O.time<applicationperiod):
+# print 'apply force @'+str(O.time)
+ O.forces.addF(i,-1*O.forces.f(i));
+
+ O.forces.addF(i,Vector3(sin(omega*O.time)*amplitude,0,0));
+# plot.addData(force=O.forces.f(i));
+
+def addplot():
+ plot.addData(force=O.forces.f(forcebodies[1])[0],pos=(O.bodies[forcebodies[1]].state.pos[0]-initialpositions[forcebodies[1]][0]),vel=O.bodies[forcebodies[1]].state.vel[0],t=O.time,time=O.time,tm=O.time)
+
+for i in forcebodies:
+ O.bodies[i].state.pos+=Vector3(0,0,0.05);
+
+## Adaptive integration engine initialization: we have given the engines in ordered, they are runned sequentally for every substep of the integrator
+
+#integratoreng=RungeKuttaCashKarp54Integrator([ ## Resets forces and momenta the act on bodies
+# ForceResetter(),
+# ## Apply internal force to the deformable elements and internal force of the interaction element
+# FEInternalForceEngine([If2_Lin4NodeTetra_LinIsoRayleighDampElast(),If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat()]),
+# PyRunner(virtPeriod=1e-99,command='applyforcetoelements()'),
+#
+#])
+# Integration tolerances of the RungeKuttaCashKarp54Integrator
+#~
+#~ integratoreng.rel_err=1e-6;
+#~
+#~ integratoreng.abs_err=1e-6;
+
+# We use only the integrator engine
+
+# Time step determines the exiting period of the integrator since the integrator performs one step from current_time to current_time+dt; using many substeps for any value of dt; then stops.
+
+O.dt=1e-8;
+
+O.engines=[
+ ForceResetter(),
+ ## Apply internal force to the deformable elements and internal force of the interaction element
+ FEInternalForceEngine([If2_Lin4NodeTetra_LinIsoRayleighDampElast(),If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat()]),
+ PyRunner(iterPeriod=1,command='applyforcetoelements()'),
+ NewtonIntegrator(damping=0,gravity=[0,0,0]),
+# ## Plotting data: adds plots after one step of the integrator engine
+ PyRunner(iterPeriod=1,command='addplot()')
+
+
+];
+#Tolerances can be set for the optimum accuracy
+
+
+from yade import plot
+
+plot.plots={'t':'vel','time':'pos','tm':'force'}
+plot.plot(subPlots=True)
+
+try:
+ from yade import qt
+ qt.View()
+ qt.Controller()
+except ImportError: pass
+
=== added file 'examples/deformableelem/testDeformableBodies_pressure.py'
--- examples/deformableelem/testDeformableBodies_pressure.py 1970-01-01 00:00:00 +0000
+++ examples/deformableelem/testDeformableBodies_pressure.py 2016-01-07 17:49:32 +0000
@@ -0,0 +1,199 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# Created by Burak ER
+
+#****** This is the test application of Longitudinal Wave propagation on Deformable Elements
+
+#****** The application is consisted of a free-fixed 1 meter rod having a miliseconds sinusoidal pressure applied on the one side.
+
+#****** The propagation of the wave is investigated.
+from yade.deformableelementsutils import *;
+
+O=Omega()
+
+## Create deformable elements internal materials and interaction element material
+
+mat=LinIsoRayleighDampElastMat(label='aluminiummaterial');# deformable body material
+
+intermat=LinCohesiveStiffPropDampElastMat(label='intermat') # deformable bodies interaction material
+
+intermat.youngmodulus=72800e6; #interaction material stiffness
+
+mat.density=2789; # deformable body density
+
+mat.youngmodulus=72800e7# deformable body youngs modulus
+
+O.materials.append(intermat)# add interaction material to list
+
+O.materials.append(mat)# add deformable body material to list
+
+## Generate and add deformable elements into scene using GMSH2 mesh:
+
+# arg1 : mesh file
+# arg2 : deformable element type
+# arg3 : deformable element material
+# arg4 : interaction element type
+# arg5 : interaction element material
+modelmesh=tetrahedral_mesh_generator('model.msh',Lin4NodeTetra,'aluminiummaterial',Lin4NodeTetra_Lin4NodeTetra_InteractionElement,'intermat')
+
+## Define the body boundary force-> it is pressure applied on the one end of the rod
+
+# x position limits of bodies that are subject to the force
+force_tail_body_lowerlimit=-1.01;
+
+force_tail_body_upperlimit=-0.9999;
+
+# Pressure Properties
+
+#pressure=Vector3(1.5e6,0,0);
+
+pressure=Vector3(1.5e8,0,0);
+
+period=(3e-4)
+
+omega=2*pi/period;
+
+applicationperiod=period/2;
+
+# Displacement Properties(Displacement Application)
+
+boundary_displacement_vector=Vector3(0.3,0,0);
+
+## Define the fixed boundary
+
+# x position limits of bodies that are subject to the fixed boundary
+
+fixed_tail_body_lowerlimit=0.99;
+
+fixed_tail_body_upperlimit=1.01;
+
+
+def getinitialpos():
+ positions=[];
+ for body in O.bodies:
+ positions.append(body.state.pos)
+ return positions
+
+
+def getboundarybodies(mesh):
+ bdy = [];
+ listofbodies = dict();
+ listofboundarybodies = dict();
+ for body in mesh:
+ if (len(body) > 1):
+ listofbodies[body[0].id] = [];
+ for bdyy in body[1]:
+ if (bdyy.shape.dispIndex == 12):
+ if (bdyy.state.pos[0] < fixed_tail_body_upperlimit):
+ if (bdyy.state.pos[0] > fixed_tail_body_lowerlimit):
+ listofbodies[body[0].id].append(bdyy); #add node to boundary bodies of body
+ if (listofbodies[body[0].id].index(
+ bdyy) == 2): #if this body has three nodes of it on the boundary then add it to the traction force list.
+ listofboundarybodies[body[0].id] = listofbodies[body[0].id];
+ return listofboundarybodies;
+
+
+def getforcebodies(mesh):
+ bdy = [];
+ listofbodies = dict();
+ listofboundarybodies = dict();
+ for body in mesh:
+ if(len(body) > 1):
+ listofbodies[body[0].id] = [];
+ for bdyy in body[1]:
+ if (bdyy.shape.dispIndex == 12):
+ if (bdyy.state.pos[0] < force_tail_body_upperlimit):
+ if (bdyy.state.pos[0] > force_tail_body_lowerlimit):
+ listofbodies[body[0].id].append(bdyy); #add node to boundary bodies of body
+ if (listofbodies[body[0].id].index(
+ bdyy) == 2): #if this body has three nodes of it on the boundary then add it to the traction force list.
+ listofboundarybodies[body[0].id] = listofbodies[body[0].id];
+
+
+ return listofboundarybodies;
+
+initialpositions=getinitialpos();
+
+forcebodies=getforcebodies(modelmesh);
+
+boundarybodies=getboundarybodies(modelmesh);
+
+def displaceelements():
+ for deformablebody in forcebodies:
+ for node in forcebodies[deformablebody]:
+ if(O.time<applicationperiod):
+ O.bodies[node.id].state.pos=O.bodies[node.id].state.pos+boundary_displacement_vector*sin(omega*O.time);
+
+## definition of functions
+def fixboundaryelements():
+ for deformablebody in boundarybodies:
+ for node in boundarybodies[deformablebody]:
+ O.forces.addF(node.id,-O.forces.f(node.id))
+ O.forces.addT(node.id,-O.forces.m(node.id))
+
+def applyforcetoelements():
+
+ for deformablebody in forcebodies:
+ pos0=O.bodies[forcebodies[deformablebody][0].id].state.pos;
+ pos1=O.bodies[forcebodies[deformablebody][1].id].state.pos;
+ pos2=O.bodies[forcebodies[deformablebody][2].id].state.pos;
+ area=((pos1-pos0).cross(pos2-pos0)).norm();
+
+ T=area*pressure;
+
+ for node in forcebodies[deformablebody]:
+ if(O.time<applicationperiod):
+ O.forces.addF(node.id,(T/3)*sin(omega*O.time));
+# fixboundaryelements();
+
+def addplot():
+ forcenode=forcebodies[forcebodies.keys()[0]][0].id;
+ boundarynode=boundarybodies[boundarybodies.keys()[0]][0].id;
+ plot.addData(force=O.forces.f(forcenode)[0],pos=(O.bodies[forcenode].state.pos[0]-initialpositions[forcenode][0]),vel=O.bodies[forcenode].state.vel[0],postail=(O.bodies[boundarynode].state.pos[0]-initialpositions[boundarynode][0]),t=O.time,time=O.time,tm=O.time,tt=O.time)
+
+
+
+
+## Adaptive integration engine initialization: we have given the engines in ordered, they are runned sequentally for every substep of the integrator
+
+integratoreng=RungeKuttaCashKarp54Integrator([ ## Resets forces and momenta the act on bodies
+ ForceResetter(),
+ ## Apply internal force to the deformable elements and internal force of the interaction element
+ FEInternalForceEngine([If2_Lin4NodeTetra_LinIsoRayleighDampElast(),If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat()]),
+ PyRunner(virtPeriod=1e-99,command='applyforcetoelements()'),
+
+])
+# Integration tolerances of the RungeKuttaCashKarp54Integrator
+
+integratoreng.rel_err=1e-3;
+
+integratoreng.abs_err=1e-3;
+
+# We use only the integrator engine
+
+# Time step determines the exiting period of the integrator since the integrator performs one step from current_time to current_time+dt;
+
+O.dt=1e-3;
+
+O.engines=[
+# integratoreng,
+ ForceResetter(),
+# ## Apply internal force to the deformable elements and internal force of the interaction element
+ FEInternalForceEngine([If2_Lin4NodeTetra_LinIsoRayleighDampElast(),If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat()]),
+ PyRunner(iterPeriod=1,command='applyforcetoelements()'),
+ NewtonIntegrator(damping=0,gravity=[0,0,0]),
+# ## Plotting data: adds plots after one step of the integrator engine
+ PyRunner(iterPeriod=1,command='addplot()')
+ ]
+
+from yade import plot
+
+plot.plots={'t':'vel','time':'pos','tm':'force','tt':'postail'}
+plot.plot(subPlots=True)
+
+try:
+ from yade import qt
+ qt.View()
+ qt.Controller()
+except ImportError: pass
+
=== added directory 'pkg/dem/deformablecohesive'
=== added file 'pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.cpp'
--- pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,77 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#include <pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.hpp>
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+#include <pkg/common/Aabb.hpp>
+
+void Bo1_DeformableElement_Aabb::go(const shared_ptr<Shape>& cm, shared_ptr<Bound>& bv, const Se3r& se3, const Body* b){
+
+ DeformableElement* deformableElement = static_cast<DeformableElement*>(cm.get());
+
+ if(!bv){ bv=shared_ptr<Bound>(new Aabb); }
+
+ Aabb* aabb=static_cast<Aabb*>(bv.get());
+
+ Vector3r min,max;
+ //Not sure this is the best of all possible algorithms, therefore, I think it can be improved
+ for (DeformableElement::NodeMap::iterator it = deformableElement->localmap.begin(); it != deformableElement->localmap.end(); it++)
+ {
+ if(it->first->state->pos(0)<min(0))
+ {
+ min(0)=it->first->state->pos(0);
+ }
+ if(it->first->state->pos(1)<min(1))
+ {
+ min(1)=it->first->state->pos(1);
+ }
+ if(it->first->state->pos(0)<min(2))
+ {
+ min(2)=it->first->state->pos(2);
+ }
+
+ if(it->first->state->pos(0)>max(0))
+ {
+ max(0)=it->first->state->pos(0);
+ }
+ if(it->first->state->pos(1)>max(1))
+ {
+ max(1)=it->first->state->pos(1);
+ }
+ if(it->first->state->pos(2)>max(2))
+ {
+ max(2)=it->first->state->pos(2);
+ }
+
+ }
+
+
+ aabb->min=min;
+ aabb->max=max;
+
+// if(!scene->isPeriodic){
+// aabb->min=se3.position-halfSize; aabb->max=se3.position+halfSize;
+// return;
+// }
+// // adjust box size along axes so that DeformableElement doesn't stick out of the box even if sheared (i.e. parallelepiped)
+// if(scene->cell->hasShear()) {
+// Vector3r refHalfSize(halfSize);
+// const Vector3r& cos=scene->cell->getCos();
+// for(int i=0; i<3; i++){
+// //cerr<<"cos["<<i<<"]"<<cos[i]<<" ";
+// int i1=(i+1)%3,i2=(i+2)%3;
+// halfSize[i1]+=.5*refHalfSize[i1]*(1/cos[i]-1);
+// halfSize[i2]+=.5*refHalfSize[i2]*(1/cos[i]-1);
+// }
+// }
+// //cerr<<" || "<<halfSize<<endl;
+// aabb->min = scene->cell->unshearPt(se3.position)-halfSize;
+// aabb->max = scene->cell->unshearPt(se3.position)+halfSize;
+}
+
+YADE_PLUGIN((Bo1_DeformableElement_Aabb));
=== added file 'pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.hpp'
--- pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,26 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#pragma once
+
+#include <pkg/common/Dispatching.hpp>
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+
+class Bo1_DeformableElement_Aabb : public BoundFunctor
+{
+ public :
+ void go(const shared_ptr<Shape>& cm, shared_ptr<Bound>& bv, const Se3r&, const Body*);
+ FUNCTOR1D(DeformableElement);
+ YADE_CLASS_BASE_DOC_ATTRS(Bo1_DeformableElement_Aabb,BoundFunctor,"Functor creating :yref:`Aabb` from :yref:`DeformableElement`.",
+ ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.\n\n.. note::\n\tThis attribute is used to create distant interaction, but is only meaningful with an :yref:`IGeomFunctor` which will not simply discard such interactions: :yref:`Ig2_Sphere_Sphere_ScGeom::interactionDetectionFactor` should have the same value as :yref:`aabbEnlargeFactor<Bo1_Sphere_Aabb::aabbEnlargeFactor>`."))
+ );
+};
+
+REGISTER_SERIALIZABLE(Bo1_DeformableElement_Aabb);
+
+
=== added file 'pkg/dem/deformablecohesive/Bo1_Node_Aabb.cpp'
--- pkg/dem/deformablecohesive/Bo1_Node_Aabb.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Bo1_Node_Aabb.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,38 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#include <pkg/dem/deformablecohesive/Bo1_Node_Aabb.hpp>
+#include <pkg/dem/deformablecohesive/Node.hpp>
+#include <pkg/common/Aabb.hpp>
+
+void Bo1_Node_Aabb::go(const shared_ptr<Shape>& cm, shared_ptr<Bound>& bv, const Se3r& se3, const Body* b){
+ Node* node = static_cast<Node*>(cm.get());
+ if(!bv){ bv=shared_ptr<Bound>(new Aabb); }
+ Aabb* aabb=static_cast<Aabb*>(bv.get());
+ Vector3r halfSize = (aabbEnlargeFactor>0?aabbEnlargeFactor:1.)*Vector3r(node->radius,node->radius,node->radius);
+ if(!scene->isPeriodic){
+ aabb->min=se3.position-halfSize; aabb->max=se3.position+halfSize;
+ return;
+ }
+ // adjust box size along axes so that Node doesn't stick out of the box even if sheared (i.e. parallelepiped)
+ if(scene->cell->hasShear()) {
+ Vector3r refHalfSize(halfSize);
+ const Vector3r& cos=scene->cell->getCos();
+ for(int i=0; i<3; i++){
+ //cerr<<"cos["<<i<<"]"<<cos[i]<<" ";
+ int i1=(i+1)%3,i2=(i+2)%3;
+ halfSize[i1]+=.5*refHalfSize[i1]*(1/cos[i]-1);
+ halfSize[i2]+=.5*refHalfSize[i2]*(1/cos[i]-1);
+ }
+ }
+ //cerr<<" || "<<halfSize<<endl;
+ aabb->min = scene->cell->unshearPt(se3.position)-halfSize;
+ aabb->max = scene->cell->unshearPt(se3.position)+halfSize;
+}
+
+YADE_PLUGIN((Bo1_Node_Aabb));
=== added file 'pkg/dem/deformablecohesive/Bo1_Node_Aabb.hpp'
--- pkg/dem/deformablecohesive/Bo1_Node_Aabb.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Bo1_Node_Aabb.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,26 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#pragma once
+
+#include <pkg/common/Dispatching.hpp>
+#include <pkg/dem/deformablecohesive/Node.hpp>
+
+class Bo1_Node_Aabb : public BoundFunctor
+{
+ public :
+ void go(const shared_ptr<Shape>& cm, shared_ptr<Bound>& bv, const Se3r&, const Body*);
+ FUNCTOR1D(Node);
+ YADE_CLASS_BASE_DOC_ATTRS(Bo1_Node_Aabb,BoundFunctor,"Functor creating :yref:`Aabb` from :yref:`Node`.",
+ ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.\n\n.. note::\n\tThis attribute is used to create distant interaction, but is only meaningful with an :yref:`IGeomFunctor` which will not simply discard such interactions: :yref:`Ig2_Sphere_Sphere_ScGeom::interactionDetectionFactor` should have the same value as :yref:`aabbEnlargeFactor<Bo1_Sphere_Aabb::aabbEnlargeFactor>`."))
+ );
+};
+
+REGISTER_SERIALIZABLE(Bo1_Node_Aabb);
+
+
=== added file 'pkg/dem/deformablecohesive/CohesiveMat.cpp'
--- pkg/dem/deformablecohesive/CohesiveMat.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/CohesiveMat.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,14 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#include <pkg/dem/deformablecohesive/CohesiveMat.hpp>
+YADE_PLUGIN((CohesiveDeformableElementMaterial)(LinCohesiveElasticMaterial)(LinCohesiveStiffPropDampElastMat));
+
+CohesiveDeformableElementMaterial::~CohesiveDeformableElementMaterial(void){}
+LinCohesiveElasticMaterial::~LinCohesiveElasticMaterial(void){}
+LinCohesiveStiffPropDampElastMat::~LinCohesiveStiffPropDampElastMat(void){}
+
=== added file 'pkg/dem/deformablecohesive/CohesiveMat.hpp'
--- pkg/dem/deformablecohesive/CohesiveMat.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/CohesiveMat.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,48 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#pragma once
+#include <core/Material.hpp>
+#include <limits>
+/*! Elastic material */
+class CohesiveDeformableElementMaterial: public Material{
+ public:
+ virtual ~CohesiveDeformableElementMaterial();
+ YADE_CLASS_BASE_DOC_ATTRS_CTOR(CohesiveDeformableElementMaterial,Material,"Deformable Element Material.",
+ // ((Real,density,1,,"Density of the material."))
+ ,
+ /*ctor*/ createIndex();
+ );
+ REGISTER_CLASS_INDEX(CohesiveDeformableElementMaterial,Material);
+};
+REGISTER_SERIALIZABLE(CohesiveDeformableElementMaterial);
+
+class LinCohesiveElasticMaterial: public CohesiveDeformableElementMaterial{
+ public:
+ virtual ~LinCohesiveElasticMaterial();
+ YADE_CLASS_BASE_DOC_ATTRS_CTOR(LinCohesiveElasticMaterial,CohesiveDeformableElementMaterial,"Linear Isotropic Elastic material",
+ ((Real,youngmodulus,.78e5,,"Young's modulus. Initially aluminium."))
+ ((Real,poissonratio,.33,,"Poisson ratio. Initially aluminium.")),
+ createIndex();
+ );
+ REGISTER_CLASS_INDEX(LinCohesiveElasticMaterial,CohesiveDeformableElementMaterial);
+};
+REGISTER_SERIALIZABLE(LinCohesiveElasticMaterial);
+
+
+/*Stiffness proportional damping material*/
+class LinCohesiveStiffPropDampElastMat: public LinCohesiveElasticMaterial{
+ public:
+ virtual ~LinCohesiveStiffPropDampElastMat();
+ YADE_CLASS_BASE_DOC_ATTRS_CTOR(LinCohesiveStiffPropDampElastMat,LinCohesiveElasticMaterial,"Elastic material with Rayleigh Damping.",
+ ((Real,alpha,0,,"Mass propotional damping constant of Rayleigh Damping."))
+ ((Real,beta,0,,"Stiffness propotional damping constant of Rayleigh Damping.")),
+ createIndex();
+ );
+ REGISTER_CLASS_INDEX(LinCohesiveStiffPropDampElastMat,LinCohesiveElasticMaterial);
+};
+REGISTER_SERIALIZABLE(LinCohesiveStiffPropDampElastMat);
=== added file 'pkg/dem/deformablecohesive/DeformableCohesiveElement.cpp'
--- pkg/dem/deformablecohesive/DeformableCohesiveElement.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/DeformableCohesiveElement.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,54 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#include <algorithm>
+#include <core/Scene.hpp>
+#include <pkg/dem/deformablecohesive/DeformableCohesiveElement.hpp>
+#include <core/BodyContainer.hpp>
+#include <core/State.hpp>
+#include <pkg/common/Sphere.hpp>
+#include <pkg/dem/deformablecohesive/Node.hpp>
+#include <lib/base/Math.hpp>
+
+DeformableCohesiveElement::~DeformableCohesiveElement(){
+
+}
+YADE_PLUGIN((DeformableCohesiveElement));
+CREATE_LOGGER(DeformableCohesiveElement);
+void DeformableCohesiveElement::addPair(const shared_ptr<Body>& nodeBody1,const shared_ptr<Body>& nodeBody2)
+{
+
+
+ const shared_ptr<Node> node1=YADE_PTR_CAST<Node>(nodeBody1->shape);//Should be checked dynamically otherwise it will always cast: every shape is castable to Node shape
+ const shared_ptr<Node> node2=YADE_PTR_CAST<Node>(nodeBody2->shape);//Should be checked dynamically otherwise it will always cast: every shape is castable to Node shape
+
+ Body::id_t subId1=nodeBody1->getId();
+ Body::id_t subId2=nodeBody2->getId();
+
+ if(node1||node2){} else{ throw std::invalid_argument(("One of the nodes that is given is not a Node therefore cannot be added to the cohesive deformable element "));}
+
+ if(subId1<0||subId2<0){throw std::invalid_argument(("One of the node that is given is not a member of the scene therefore it has no state, not adding exiting"));}
+
+ if(this->localmap.count(nodeBody1)!=0) throw std::invalid_argument(("Node that has Body id #"+boost::lexical_cast<string>(subId1)+" is already part of this cohesive deformable element"));
+ if(this->localmap.count(nodeBody2)!=0) throw std::invalid_argument(("Node that has Body id #"+boost::lexical_cast<string>(subId2)+" is already part of this cohesive deformable element"));
+
+ nodepair pair;
+ pair.node1=nodeBody1;
+ pair.node2=nodeBody2;
+ this->nodepairs[pair]=Se3r();
+ // Add body to localmap
+ this->nodepairs[pair].position=nodeBody1->state->pos-nodeBody2->state->pos;// Initial difference on positions
+
+ return;
+
+}
+void DeformableCohesiveElement::delPair(const shared_ptr<Body>& node1,const shared_ptr<Body>& node2)
+{
+ // erase the subBody; removing body that is not part of the element throws
+// if(this->localmap.erase(subBody)!=1) throw std::invalid_argument(("Node #"+boost::lexical_cast<string>(subBody->id)+" not a part of the deformable element, not removing...").c_str());
+// LOG_DEBUG("Removed node #"<<subBody->id);
+}
=== added file 'pkg/dem/deformablecohesive/DeformableCohesiveElement.hpp'
--- pkg/dem/deformablecohesive/DeformableCohesiveElement.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/DeformableCohesiveElement.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,82 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#pragma once
+
+#include <core/Body.hpp>
+#include <core/PartialEngine.hpp>
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+#include <lib/base/Logging.hpp>
+#include <lib/base/Math.hpp>
+
+//#include <yade/trunk/pkg/dem/deformablecohesive/Node.hpp> //Node shape
+
+/* Before starting the implementation of the deformable element, I am really dissappointed that deformableelement's algorithm relies on its shape.
+Shape means "shape" and I think it should not contain any other physical meaning or anything else.
+
+With respect to this view; The deformable element class is derived from the body and knows the information of
+its members that are node shaped bodies.
+
+*/
+
+//class NewtonIntegrator;
+
+class DeformableCohesiveElement: public DeformableElement {
+ public:
+
+ struct nodepair:public Serializable{
+ public:
+
+ YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(nodepair,Serializable,"Geometry of a body",
+ ((shared_ptr<Body>,node1,,,"Node1 of node pair"))
+ ((shared_ptr<Body>,node2,,,"Node2 of node pair")),
+ /*ctor*/,
+ /*py*/
+ );
+
+ // Comparison operator for table sorting.
+ bool operator<(const nodepair& param) const
+ {
+ if (node1.get() < param.node1.get()) return true;
+ if (node1.get() > param.node1.get()) return false;
+ if (node2.get() < param.node2.get()) return true;
+ if (node2.get() > param.node2.get()) return false;
+ }
+ };
+
+ typedef std::map<nodepair,Se3r> NodePairsMap;//Initial node differences
+ typedef std::map<Vector3r,Se3r> localTriad;//Updated on every step
+ unsigned int max_pair;
+ Matrix calculateStiffness(Real, Real ,Vector3r,Vector3r,Vector3r,Vector3r);
+ Matrix calculateMassMatrix(Real, Real);
+ virtual ~DeformableCohesiveElement();
+ void initialize(void){max_pair=3;}
+
+ void addPair(const shared_ptr<Body>& node1,const shared_ptr<Body>& node2);
+ void delPair(const shared_ptr<Body>& node1,const shared_ptr<Body>& node2);
+
+ YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(DeformableCohesiveElement,DeformableElement,"Tetrahedral Deformable Element Composed of Nodes",
+ ((NodePairsMap,nodepairs,,,"Ids and relative position+orientation difference of members of the cohesive deformable element in the inital condition (should not be accessed directly)"))
+ ,
+ ,
+ createIndex(); /*ctor*/
+ initialize();
+ ,
+ /*py*/
+ .def("addPair",&DeformableCohesiveElement::addPair,"Add a node shared_pt<:yref:'Body'>& as into the element")
+ .def("removePair",&DeformableCohesiveElement::delPair,"Add a node shared_pt<:yref:'Body'>& as into the element")
+ );
+ DECLARE_LOGGER;
+
+ REGISTER_CLASS_INDEX(DeformableCohesiveElement,DeformableElement);
+
+};
+
+// necessary
+using namespace yade;
+REGISTER_SERIALIZABLE(DeformableCohesiveElement);
=== added file 'pkg/dem/deformablecohesive/DeformableElement.cpp'
--- pkg/dem/deformablecohesive/DeformableElement.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/DeformableElement.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,103 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+#include <algorithm>
+#include <core/Scene.hpp>
+#include <core/BodyContainer.hpp>
+#include <core/State.hpp>
+#include <pkg/common/Sphere.hpp>
+#include <pkg/dem/deformablecohesive/Node.hpp>
+#include <string.h>
+#include <boost/lexical_cast.hpp>
+
+DeformableElement::~DeformableElement(){
+
+}
+YADE_PLUGIN((DeformableElement));
+
+boost::python::dict DeformableElement::localmap_get(){
+ boost::python::dict ret;
+ FOREACH(NodeMap::value_type& b, localmap){
+ ret[b.first]=boost::python::make_tuple(b.second.position,b.second.orientation);
+ }
+ return ret;
+}
+void DeformableElement::addFace(Vector3r& indexes){
+
+ faces.push_back(indexes);
+
+}
+//std::vector<Vector3r> DeformableElement::getDisplacements(void)
+//{
+//
+//}
+shared_ptr<Body> DeformableElement::getNode(int id){
+
+ NodeMap::iterator i1(this->localmap.begin());
+ std::advance(i1,id);
+ return i1->first;
+
+}
+
+void DeformableElement::removeLastFace(void){
+
+ faces.pop_back();
+
+}
+
+void DeformableElement::addNode(const shared_ptr<Body>& nodeBody){
+
+
+ if(this->localmap.size()==maxNodeCount)
+ {
+ std::string errormessage ="This element cannot hold more than"+ boost::lexical_cast<std::string>(maxNodeCount);
+ throw std::out_of_range(errormessage);
+ return;
+ }
+ const shared_ptr<Node> node=YADE_PTR_CAST<Node>(nodeBody->shape);//Should be checked dynamically otherwise it will always cast: every shape is castable to Node shape
+
+ Body::id_t subId=nodeBody->getId();
+
+ if(node){} else{ throw std::invalid_argument(("The body that is given #"+boost::lexical_cast<string>(subId)+" is not a Node therefore cannot be added to the deformable element "));}
+
+ if(subId<0){throw std::invalid_argument(("The Node that is given is not a member of the scene therefore it has no state, not adding exiting"));}
+
+ if(this->localmap.count(nodeBody)!=0) throw std::invalid_argument(("Node that has Body id #"+boost::lexical_cast<string>(subId)+" is already part of this deformable element"));
+
+ // Add body to localmap
+ this->localmap[nodeBody]=Se3r();// meaningful values will be put in by DeformableElement::updateProperties
+
+ // Get first node
+ //Scene* scene(Omega::instance().getScene().get()); // get scene
+ //const shared_ptr<Body>& member=localmap.begin()->first;
+
+ //Substract from the current node, therefore find the local value,
+ localmap[nodeBody].position=nodeBody->state->pos;
+
+
+ //cout<<"Local map of "<<subId<<" is ="<<localmap[subId].position;
+ //localmap[subId].orientation=nodeBody->state->ori;
+
+ //this->setBounded(false); // disallow collisions with the element itself
+
+ //If we have more than three nodes define a local triad that is clumped on the first node and initially parallel to the global frame
+ if(this->localmap.size()>=3)
+ {
+ //define a local triad if needed
+ }
+
+ return;
+}
+
+void DeformableElement::delNode(const shared_ptr<Body>& subBody){
+ // erase the subBody; removing body that is not part of the element throws
+ if(this->localmap.erase(subBody)!=1) throw std::invalid_argument(("Node #"+boost::lexical_cast<string>(subBody->id)+" not a part of the deformable element, not removing...").c_str());
+ LOG_DEBUG("Removed node #"<<subBody->id);
+}
+
+
=== added file 'pkg/dem/deformablecohesive/DeformableElement.hpp'
--- pkg/dem/deformablecohesive/DeformableElement.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/DeformableElement.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,92 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#pragma once
+
+#include <core/Body.hpp>
+#include <core/PartialEngine.hpp>
+#include <core/Shape.hpp>
+#include <lib/base/Logging.hpp>
+#include <lib/base/Math.hpp>
+
+//#include <yade/trunk/pkg/dem/deformablecohesive/Node.hpp> //Node shape
+
+/* Before starting the implementation of the deformable element, I am really dissappointed that deformableelement's algorithm relies on its shape.
+Shape means "shape" and I think it should not contain any other physical meaning or anything else.
+
+With respect to this view; The deformable element class is derived from the body and knows the information of
+its members that are node shaped bodies.
+
+*/
+
+class NewtonIntegrator;
+class InternalForceFunctor;
+namespace yade{
+typedef Eigen::MatrixXd Matrix;
+
+class DeformableElement: public Shape {
+ public:
+
+ typedef std::map<shared_ptr<Body>,Se3r> NodeMap;//Node id's with initial positions first node is selected as the reference node
+ typedef std::vector<Vector3r> Triangles; // Used for drawing the element
+
+ unsigned int maxNodeCount;//Maximum number of nodes of this element
+ Se3r referenceCoord;//Reference node position in global coordinates
+
+ virtual ~DeformableElement();
+ void addNode(const shared_ptr<Body>& subBody);
+ shared_ptr<Body> getNode(int id);
+
+ void delNode(const shared_ptr<Body>& subBody);
+ std::vector<Vector3r> getDisplacements(void);
+
+ void addFace(Vector3r&);
+ void removeLastFace(void);
+ //! Recalculate physical properties of DeformableElement.
+ //virtual void getMassMatrix()=0;
+
+ Se3r frame_get() const
+ {
+ const shared_ptr<Body>& member=localmap.begin()->first;
+ return member->state->se3;
+ }
+
+ void frame_set(Se3r) const
+ {
+ return;
+ }
+
+ boost::python::dict localmap_get();
+
+ virtual Real getVolume(){return -1;}
+ YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(DeformableElement,Shape,"Deformable aggregate of nodes",
+ ((NodeMap,localmap,,,"Ids and relative positions+orientations of members of the deformable element (should not be accessed directly)"))
+ ((Se3r,elementframe,,,"Position and orientation of the element frame"))
+ ((Triangles,faces,,,"Faces of the element for drawing"))
+ ,
+ ,
+ createIndex(); /*ctor*/
+ //init();
+ ,
+ /*py*/
+ .add_property("elementframe",&DeformableElement::frame_get)
+ .def("addNode",&DeformableElement::addNode,"Add a node shared_pt<:yref:'Body'>& as into the element")
+ .def("getNode",&DeformableElement::getNode,"Get a node shared_pt<:yref:'Body'>& as into the element")
+ .def("delNode",&DeformableElement::delNode,"Remove a node shared_pt<:yref:'Body'>& from the element")
+ .def("addFace",&DeformableElement::addFace,"Add a face into the element")
+ .def("removeLastFace",&DeformableElement::removeLastFace,"Remove a face from the element")
+ .def("getVolume",&DeformableElement::getVolume,"Get volume of the element")
+
+ );
+ REGISTER_CLASS_INDEX(DeformableElement,Shape);
+
+};
+}
+// necessary
+using namespace yade;
+REGISTER_SERIALIZABLE(DeformableElement);
=== added file 'pkg/dem/deformablecohesive/FEInternalForceDispatchers.cpp'
--- pkg/dem/deformablecohesive/FEInternalForceDispatchers.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/FEInternalForceDispatchers.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,35 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+#include <pkg/dem/deformablecohesive/FEInternalForceDispatchers.hpp>
+YADE_PLUGIN((InternalForceFunctor)(InternalForceDispatcher));
+InternalForceFunctor::~InternalForceFunctor(){};
+
+
+/********************************************************************
+ InternalForceDispatcher
+*********************************************************************/
+
+CREATE_LOGGER(InternalForceDispatcher);
+void InternalForceDispatcher::action()
+{
+ //There is no need to make an action for this dispatcher its main misson is to return functors for the shape that is given.
+}
+//void InternalForceDispatcher::explicitAction(const shared_ptr<DeformableElement> deformableelement,const Body* bdy){
+//
+// updateScenePtr();
+// shared_ptr<DeformableElement> deformableElement=deformableelement;
+// if(!deformableElement->functorCache.iff){
+// deformableElement->functorCache.iff=getFunctor1D(deformableElement);
+// if(!deformableElement->functorCache.iff) throw invalid_argument("InternalForceDispatcher::explicitAction did not find a suitable dispatch for type"+deformableElement->getClassName());
+// deformableElement->functorCache.iff->go(deformableElement,bdy);
+// }
+//
+//
+//}
+
=== added file 'pkg/dem/deformablecohesive/FEInternalForceDispatchers.hpp'
--- pkg/dem/deformablecohesive/FEInternalForceDispatchers.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/FEInternalForceDispatchers.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,50 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER burak.er@xxxxxxxxxx *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#pragma once
+#include <core/Shape.hpp>
+#include <lib/base/Math.hpp>
+#include <core/Interaction.hpp>
+#include <core/Scene.hpp>
+#include <core/State.hpp>
+#include <core/Shape.hpp>
+#include <core/IGeom.hpp>
+#include <core/IPhys.hpp>
+#include <core/Functor.hpp>
+#include <core/Dispatcher.hpp>
+#include <pkg/common/Aabb.hpp>
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+
+
+/*Functor of Internal Force Calculation*/
+
+class InternalForceFunctor: public Functor2D<
+ /*dispatch types*/ Shape,
+ Material,
+ /*return type*/ void ,
+ /*argument types*/ TYPELIST_3(const shared_ptr<Shape>&,const shared_ptr<Material>&,const shared_ptr<Body>&)
+>{
+ public: virtual ~InternalForceFunctor();
+ YADE_CLASS_BASE_DOC(InternalForceFunctor,Functor,"Functor for creating/updating :yref:`Body::bound`.");
+};
+REGISTER_SERIALIZABLE(InternalForceFunctor);
+
+/*Dispatcher of Internal Force Functors*/
+class InternalForceDispatcher: public Dispatcher2D<
+ /* functor type*/ InternalForceFunctor
+>{
+ public:
+ virtual void action();
+ // void explicitAction(const shared_ptr<DeformableElement>& deformableelement,const Body* bdy);
+
+ //virtual bool isActivated(){ return activated; }
+ DECLARE_LOGGER;
+ YADE_DISPATCHER2D_FUNCTOR_DOC_ATTRS_CTOR_PY(InternalForceDispatcher,InternalForceFunctor,/*doc is optional*/,/*attrs*/,/*ctor*/,/*py*/);
+};
+REGISTER_SERIALIZABLE(InternalForceDispatcher);
+
=== added file 'pkg/dem/deformablecohesive/FEInternalForceEngine.cpp'
--- pkg/dem/deformablecohesive/FEInternalForceEngine.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/FEInternalForceEngine.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,90 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+#include <pkg/dem/deformablecohesive/FEInternalForceDispatchers.hpp>
+#include <pkg/dem/deformablecohesive/FEInternalForceEngine.hpp>
+
+YADE_PLUGIN((FEInternalForceEngine));
+CREATE_LOGGER(FEInternalForceEngine);
+
+void FEInternalForceEngine::pyHandleCustomCtorArgs(boost::python::tuple& t, boost::python::dict& d){
+ cout<<"Entered the initialization function";
+ if(boost::python::len(t)==0) return; // nothing to do
+
+ if(boost::python::len(t)!=1) throw invalid_argument("At least 1 functors must be given");
+
+
+
+ boost::python::list vv=boost::python::extract<boost::python::list>(t[0])();
+
+// FOREACH(shared_ptr<InternalForceFunctor> iff, vv) this->internalforcedispatcher->add(iff);
+
+ for( int i=0;i<len(vv);i++) this->internalforcedispatcher->add(boost::python::extract<shared_ptr<InternalForceFunctor>>(vv[i]));
+
+
+ t=boost::python::tuple(); // empty the args; not sure if this is OK, as there is some refcounting in raw_constructor code
+ cout<<"Added to the list";
+}
+
+
+void FEInternalForceEngine::action(){
+
+ // update Scene* of the dispatcher
+ internalforcedispatcher->scene=scene;
+ // ask dispatcher to update Scene* of their functors
+ internalforcedispatcher->updateScenePtr();
+
+ // call InternalForceFunctor::preStep
+ //FOREACH(const shared_ptr<InternalForceFunctor>& iff, internalforcedispatcher->functors) iff->preStep();
+
+ /*
+ initialize callbacks; they return pointer (used only in this timestep) to the function to be called
+ returning NULL deactivates the callback in this timestep
+ */
+// // pair of callback object and pointer to the function to be called
+// vector<IntrCallback::FuncPtr> callbackPtrs;
+// FOREACH(const shared_ptr<IntrCallback> cb, callbacks){
+// cb->scene=scene;
+// callbackPtrs.push_back(cb->stepInit());
+// }
+// assert(callbackPtrs.size()==callbacks.size());
+// size_t callbacksSize=callbacks.size();
+
+ // cache transformed cell size
+ // Matrix3r cellHsize; if(scene->isPeriodic) cellHsize=scene->cell->hSize;
+
+
+ #ifdef YADE_OPENMP
+ const long size=scene->bodies->size();
+ #pragma omp parallel for schedule(guided) num_threads(ompThreads>0 ? ompThreads : omp_get_max_threads())
+ for(long i=0; i<size; i++){
+ shared_ptr<Body>& bdy=(*scene->bodies)[i];
+ #else
+ FOREACH(const shared_ptr<Body>& bdy, *scene->bodies){
+ #endif
+
+ //Try to get internal functor
+ if(bdy->shape->internalforcefunctor.get()==0) {
+ //If there isn't any internalforcefunctor; try to get one
+ bdy->shape->internalforcefunctor=internalforcedispatcher->getFunctor(bdy->shape,bdy->material);
+ //İf we found any of them that is suitable to this element???
+ if(bdy->shape->internalforcefunctor!=0){
+ //If yes try to apply internal force functor
+ shared_ptr<DeformableElement> deformableElement=YADE_PTR_CAST<DeformableElement>(bdy->shape);
+ bdy->shape->internalforcefunctor->go(deformableElement,bdy->material,bdy);
+ }
+ }
+ else{
+ //Take functor from cache and call it's go functor
+ shared_ptr<DeformableElement> deformableElement=YADE_PTR_CAST<DeformableElement>(bdy->shape);
+ bdy->shape->internalforcefunctor->go(deformableElement,bdy->material,bdy);
+ }
+
+ }
+}
=== added file 'pkg/dem/deformablecohesive/FEInternalForceEngine.hpp'
--- pkg/dem/deformablecohesive/FEInternalForceEngine.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/FEInternalForceEngine.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,42 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER burak.er@xxxxxxxxxx *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#pragma once
+#include <core/GlobalEngine.hpp>
+#include <pkg/common/Callbacks.hpp>
+#include <pkg/dem/deformablecohesive/FEInternalForceDispatchers.hpp>
+
+#ifdef USE_TIMING_DELTAS
+ #define TIMING_DELTAS_CHECKPOINT(cpt) timingDeltas->checkpoint(cpt)
+ #define TIMING_DELTAS_START() timingDeltas->start()
+#else
+ #define TIMING_DELTAS_CHECKPOINT(cpt)
+ #define TIMING_DELTAS_START()
+#endif
+
+class FEInternalForceEngine: public GlobalEngine {
+
+// #ifdef YADE_OPENMP
+// std::vector<std::list<idPair> > eraseAfterLoopIds;
+// void eraseAfterLoop(Body::id_t id1,Body::id_t id2){ eraseAfterLoopIds[omp_get_thread_num()].push_back(idPair(id1,id2)); }
+// #else
+// list<idPair> eraseAfterLoopIds;
+// void eraseAfterLoop(Body::id_t id1,Body::id_t id2){ eraseAfterLoopIds.push_back(idPair(id1,id2)); }
+// #endif
+ public:
+ virtual void pyHandleCustomCtorArgs(boost::python::tuple& t, boost::python::dict& d);
+ virtual void action();
+ YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(FEInternalForceEngine,GlobalEngine,"Unified dispatcher for handling Finite Element internal force loop at every step, for parallel performance reasons.\n\n.. admonition:: Special constructor\n\n\tConstructs from 3 lists of :yref:`Ig2<IGeomFunctor>`, :yref:`Ip2<IPhysFunctor>`, :yref:`Law<LawFunctor>` functors respectively; they will be passed to interal dispatchers, which you might retrieve.",
+ ((shared_ptr<InternalForceDispatcher>,internalforcedispatcher,new InternalForceDispatcher,Attr::readonly,":yref:`InternalForceDispatcher` object that is used for dispatching of element types."))
+ ,
+ /*ctor*/
+ ,
+ /*py*/
+ );
+ DECLARE_LOGGER;
+};
+REGISTER_SERIALIZABLE(FEInternalForceEngine);
=== added file 'pkg/dem/deformablecohesive/Gl1_DeformableElement.cpp'
--- pkg/dem/deformablecohesive/Gl1_DeformableElement.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Gl1_DeformableElement.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,98 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#ifdef YADE_OPENGL
+
+#include <pkg/dem/deformablecohesive/Gl1_DeformableElement.hpp>
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+#include <lib/opengl/OpenGLWrapper.hpp>
+
+typedef DeformableElement::NodeMap NodeMap;
+void Gl1_DeformableElement::go(const shared_ptr<Shape>& cm, const shared_ptr<State>& ,bool wire,const GLViewInfo&)
+{
+ DeformableElement* element = static_cast<DeformableElement*>(cm.get());
+ std::vector<Vector3r> triangles = element->faces;
+
+
+ if(!(cm->wire || wire)){
+ glDisable(GL_CULL_FACE);
+ //Vector3r normal=(facet->vertices[1]-facet->vertices[0]).cross(facet->vertices[2]-facet->vertices[1]); normal.normalize();
+ glColor3v(cm->color);
+ glBegin(GL_TRIANGLES);
+
+ FOREACH(Vector3r vertices,triangles){
+ NodeMap::iterator i1(element->localmap.begin());
+ NodeMap::iterator i2(i1);
+ NodeMap::iterator i3(i1);
+ NodeMap::iterator i4(i1);
+
+ //Find the opposite vertex total indice sum equals to six therefore the last one is going to be 6-sum of indices
+ // I accept it is very uncommon
+ int oppositevertexindex=6-vertices.sum();
+
+ std::advance(i1,vertices[0]);
+ std::advance(i2,vertices[1]);
+ std::advance(i3,vertices[2]);
+ std::advance(i4,oppositevertexindex);
+
+ const shared_ptr<Body>& member1=i1->first;
+ const shared_ptr<Body>& member2=i2->first;
+ const shared_ptr<Body>& member3=i3->first;
+
+ Vector3r& vertex0=i1->first->state->pos;
+ Vector3r& vertex1=i2->first->state->pos;
+ Vector3r& vertex2=i3->first->state->pos;
+ Vector3r& vertex3=i4->first->state->pos;
+
+ Vector3r normal=(vertex1-vertex0).cross(vertex2-vertex0);
+ normal.normalize();
+
+ if((vertex3-vertex0).dot(normal)>0)
+ normal=-normal;
+
+
+ glNormal3v(normal); // this makes every triangle different WRT the light
+ glVertex3v(member1->state->pos);
+ glVertex3v(member2->state->pos);
+ glVertex3v(member3->state->pos);
+
+ }
+ }
+ glEnd();
+
+ glBegin(GL_LINE_LOOP);
+ glColor3v(Vector3r(0,0,0));
+ FOREACH(Vector3r vertices,triangles){
+
+ NodeMap::iterator i1(element->localmap.begin());
+ NodeMap::iterator i2(i1);
+ NodeMap::iterator i3(i1);
+
+ std::advance(i1,vertices[0]);
+ std::advance(i2,vertices[1]);
+ std::advance(i3,vertices[2]);
+
+ const shared_ptr<Body>& member1=i1->first;
+ const shared_ptr<Body>& member2=i2->first;
+ const shared_ptr<Body>& member3=i3->first;
+
+
+ glVertex3v(member1->state->pos);
+ glVertex3v(member2->state->pos);
+ glVertex3v(member3->state->pos);
+
+
+
+ }
+
+ glEnd();
+
+}
+
+YADE_PLUGIN((Gl1_DeformableElement));
+
+#endif /* YADE_OPENGL */
=== added file 'pkg/dem/deformablecohesive/Gl1_DeformableElement.hpp'
--- pkg/dem/deformablecohesive/Gl1_DeformableElement.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Gl1_DeformableElement.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,24 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#pragma once
+
+#include <pkg/common/GLDrawFunctors.hpp>
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+
+class Gl1_DeformableElement : public GlShapeFunctor
+{
+ public:
+ virtual void go(const shared_ptr<Shape>&, const shared_ptr<State>&,bool,const GLViewInfo&);
+ YADE_CLASS_BASE_DOC(Gl1_DeformableElement,GlShapeFunctor,"Renders :yref:`Node` object"
+ );
+ RENDERS(DeformableElement);
+};
+
+REGISTER_SERIALIZABLE(Gl1_DeformableElement);
+
+
=== added file 'pkg/dem/deformablecohesive/Gl1_Node.cpp'
--- pkg/dem/deformablecohesive/Gl1_Node.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Gl1_Node.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,182 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER burak.er@xxxxxxxxxx *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#ifdef YADE_OPENGL
+
+
+#include <pkg/dem/deformablecohesive/Gl1_Node.hpp>
+#include <lib/opengl/OpenGLWrapper.hpp>
+#include <pkg/common/Sphere.hpp>
+bool Gl1_Node::wire;
+bool Gl1_Node::stripes;
+int Gl1_Node::glutSlices;
+int Gl1_Node::glutStacks;
+Real Gl1_Node::quality;
+bool Gl1_Node::localSpecView;
+vector<Vector3r> Gl1_Node::vertices, Gl1_Node::faces;
+int Gl1_Node::glStripedSphereList=-1;
+int Gl1_Node::glGlutSphereList=-1;
+Real Gl1_Node::prevQuality=0;
+
+void Gl1_Node::go(const shared_ptr<Shape>& cm, const shared_ptr<State>& ,bool wire2, const GLViewInfo&)
+{
+ glClearDepth(1.0f);
+ glEnable(GL_NORMALIZE);
+
+ Real r=(static_cast<Sphere*>(cm.get()))->radius;
+ glColor3v(cm->color);
+ if (wire || wire2) glutWireSphere(r,quality*glutSlices,quality*glutStacks);
+ else {
+ //Check if quality has been modified or if previous lists are invalidated (e.g. by creating a new qt view), then regenerate lists
+ bool somethingChanged = (abs(quality-prevQuality)>0.001 || glIsList(glStripedSphereList)!=GL_TRUE);
+ if (somethingChanged) {initStripedGlList(); initGlutGlList(); prevQuality=quality;}
+ glScalef(r,r,r);
+ if(stripes) glCallList(glStripedSphereList);
+ else glCallList(glGlutSphereList);
+ }
+ return;
+}
+YADE_PLUGIN((Gl1_Node));
+
+void Gl1_Node::subdivideTriangle(Vector3r& v1,Vector3r& v2,Vector3r& v3, int depth){
+ Vector3r v;
+ //Change color only at the appropriate level, i.e. 8 times in total, since we draw 8 mono-color sectors one after another
+ if (depth==int(quality) || quality<=0){
+ v = (v1+v2+v3)/3.0;
+ GLfloat matEmit[4];
+ if (v[1]*v[0]*v[2]>0){
+ matEmit[0] = 0.3;
+ matEmit[1] = 0.3;
+ matEmit[2] = 0.3;
+ matEmit[3] = 1.f;
+ }else{
+ matEmit[0] = 0.15;
+ matEmit[1] = 0.15;
+ matEmit[2] = 0.15;
+ matEmit[3] = 0.2;
+ }
+ glMaterialfv(GL_FRONT, GL_EMISSION, matEmit);
+ }
+
+ if (depth==1){//Then display 4 triangles
+ Vector3r v12 = v1+v2;
+ Vector3r v23 = v2+v3;
+ Vector3r v31 = v3+v1;
+ v12.normalize();
+ v23.normalize();
+ v31.normalize();
+ //Use TRIANGLE_STRIP for faster display of adjacent facets
+ glBegin(GL_TRIANGLE_STRIP);
+ glNormal3v(v1); glVertex3v(v1);
+ glNormal3v(v31); glVertex3v(v31);
+ glNormal3v(v12); glVertex3v(v12);
+ glNormal3v(v23); glVertex3v(v23);
+ glNormal3v(v2); glVertex3v(v2);
+ glEnd();
+ //terminate with this triangle left behind
+ glBegin(GL_TRIANGLES);
+ glNormal3v(v3); glVertex3v(v3);
+ glNormal3v(v23); glVertex3v(v23);
+ glNormal3v(v31); glVertex3v(v31);
+ glEnd();
+ return;
+ }
+ Vector3r v12 = v1+v2;
+ Vector3r v23 = v2+v3;
+ Vector3r v31 = v3+v1;
+ v12.normalize();
+ v23.normalize();
+ v31.normalize();
+ subdivideTriangle(v1,v12,v31,depth-1);
+ subdivideTriangle(v2,v23,v12,depth-1);
+ subdivideTriangle(v3,v31,v23,depth-1);
+ subdivideTriangle(v12,v23,v31,depth-1);
+}
+
+void Gl1_Node::initStripedGlList() {
+ if (!vertices.size()){//Fill vectors with vertices and facets
+ //Define 6 points for +/- coordinates
+ vertices.push_back(Vector3r(-1,0,0));//0
+ vertices.push_back(Vector3r(1,0,0));//1
+ vertices.push_back(Vector3r(0,-1,0));//2
+ vertices.push_back(Vector3r(0,1,0));//3
+ vertices.push_back(Vector3r(0,0,-1));//4
+ vertices.push_back(Vector3r(0,0,1));//5
+ //Define 8 sectors of the sphere
+ faces.push_back(Vector3r(3,4,1));
+ faces.push_back(Vector3r(3,0,4));
+ faces.push_back(Vector3r(3,5,0));
+ faces.push_back(Vector3r(3,1,5));
+ faces.push_back(Vector3r(2,1,4));
+ faces.push_back(Vector3r(2,4,0));
+ faces.push_back(Vector3r(2,0,5));
+ faces.push_back(Vector3r(2,5,1));
+ }
+ //Generate the list. Only once for each qtView, or more if quality is modified.
+ glDeleteLists(glStripedSphereList,1);
+ glStripedSphereList = glGenLists(1);
+ glNewList(glStripedSphereList,GL_COMPILE);
+ glEnable(GL_LIGHTING);
+ glShadeModel(GL_SMOOTH);
+ // render the sphere now
+ for (int i=0;i<8;i++)
+ subdivideTriangle(vertices[(unsigned int)faces[i][0]],vertices[(unsigned int)faces[i][1]],vertices[(unsigned int)faces[i][2]],1+ (int) quality);
+ glEndList();
+
+}
+
+void Gl1_Node::initGlutGlList(){
+ //Generate the "no-stripes" display list, each time quality is modified
+ glDeleteLists(glGlutSphereList,1);
+ glGlutSphereList = glGenLists(1);
+ glNewList(glGlutSphereList,GL_COMPILE);
+ glEnable(GL_LIGHTING);
+ glShadeModel(GL_SMOOTH);
+ glutSolidSphere(1.0,max(quality*glutSlices,(Real)2.),max(quality*glutStacks,(Real)3.));
+ glEndList();
+}
+
+#endif /* YADE_OPENGL */
+
+// ///The old Galizzi's lists
+// if (!vertices.size()) {
+// Real X = 0.525731112119133606;
+// Real Z = 0.850650808352039932;
+// vertices.push_back(Vector3r(-X,0,Z));//0
+// vertices.push_back(Vector3r(X,0,Z));//1
+// vertices.push_back(Vector3r(-X,0,-Z));//2
+// vertices.push_back(Vector3r(X,0,-Z));//3
+// vertices.push_back(Vector3r(0,Z,X));//4
+// vertices.push_back(Vector3r(0,Z,-X));//5
+// vertices.push_back(Vector3r(0,-Z,X));//6
+// vertices.push_back(Vector3r(0,-Z,-X));//7
+// vertices.push_back(Vector3r(Z,X,0));//8
+// vertices.push_back(Vector3r(-Z,X,0));//9
+// vertices.push_back(Vector3r(Z,-X,0));//10
+// vertices.push_back(Vector3r(-Z,-X,0));//11
+// faces.push_back(Vector3r(0,4,1));
+// faces.push_back(Vector3r(0,9,4));
+// faces.push_back(Vector3r(9,5,4));
+// faces.push_back(Vector3r(4,5,8));
+// faces.push_back(Vector3r(4,8,1));
+// faces.push_back(Vector3r(8,10,1));
+// faces.push_back(Vector3r(8,3,10));
+// faces.push_back(Vector3r(5,3,8));
+// faces.push_back(Vector3r(5,2,3));
+// faces.push_back(Vector3r(2,7,3));
+// faces.push_back(Vector3r(7,10,3));
+// faces.push_back(Vector3r(7,6,10));
+// faces.push_back(Vector3r(7,11,6));
+// faces.push_back(Vector3r(11,0,6));
+// faces.push_back(Vector3r(0,1,6));
+// faces.push_back(Vector3r(6,1,10));
+// faces.push_back(Vector3r(9,0,11));
+// faces.push_back(Vector3r(9,11,2));
+// faces.push_back(Vector3r(9,2,5));
+// faces.push_back(Vector3r(7,2,11));}
+
=== added file 'pkg/dem/deformablecohesive/Gl1_Node.hpp'
--- pkg/dem/deformablecohesive/Gl1_Node.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Gl1_Node.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,40 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER burak.er@xxxxxxxxxx *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#pragma once
+
+#include <pkg/common/GLDrawFunctors.hpp>
+#include <pkg/dem/deformablecohesive/Node.hpp>
+
+
+class Gl1_Node : public GlShapeFunctor{
+ private:
+ // for stripes
+ static vector<Vector3r> vertices, faces;
+ static int glStripedSphereList;
+ static int glGlutSphereList;
+ void subdivideTriangle(Vector3r& v1,Vector3r& v2,Vector3r& v3, int depth);
+// void drawSphere(const Vector3r& color);
+ //Generate GlList for GLUT sphere
+ void initGlutGlList();
+ //Generate GlList for sliced spheres
+ void initStripedGlList();
+ //for regenerating glutSphere list if needed
+ static Real prevQuality;
+ public:
+ virtual void go(const shared_ptr<Shape>&, const shared_ptr<State>&,bool,const GLViewInfo&);
+ YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_Node,GlShapeFunctor,"Renders :yref:`Node` object",
+ ((Real,quality,1.0,,"Change discretization level of spheres. quality>1 for better image quality, at the price of more cpu/gpu usage, 0<quality<1 for faster rendering. If mono-color spheres are displayed (:yref:`Gl1_Node::stripes` = False), quality mutiplies :yref:`Gl1_Node::glutSlices` and :yref:`Gl1_Node::glutStacks`. If striped spheres are displayed (:yref:`Gl1_Node::stripes` = True), only integer increments are meaningfull : quality=1 and quality=1.9 will give the same result, quality=2 will give finer result."))
+ ((bool,wire,false,,"Only show wireframe (controlled by ``glutSlices`` and ``glutStacks``."))
+ ((bool,stripes,false,,"In non-wire rendering, show stripes clearly showing particle rotation."))
+ ((bool,localSpecView,true,,"Compute specular light in local eye coordinate system."))
+ ((int,glutSlices,12,(Attr::noSave | Attr::readonly),"Base number of sphere slices, multiplied by :yref:`Gl1_Node::quality` before use); not used with ``stripes`` (see `glut{Solid,Wire}Sphere reference <http://www.opengl.org/documentation/specs/glut/spec3/node81.html>`_)"))
+ ((int,glutStacks,6,(Attr::noSave | Attr::readonly),"Base number of sphere stacks, multiplied by :yref:`Gl1_Node::quality` before use; not used with ``stripes`` (see `glut{Solid,Wire}Sphere reference <http://www.opengl.org/documentation/specs/glut/spec3/node81.html>`_)"))
+ );
+ RENDERS(Node);
+};
+REGISTER_SERIALIZABLE(Gl1_Node);
=== added file 'pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.cpp'
--- pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,61 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER burak.er@xxxxxxxxxx *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#include <pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.hpp>
+#include <pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.hpp>
+YADE_PLUGIN((If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat));
+If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat::~If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat(){};
+
+
+/********************************************************************
+ InternalForceDispatcher
+*********************************************************************/
+typedef std::map<DeformableCohesiveElement::nodepair,Se3r> NodePairsMap;//Initial node differences
+
+CREATE_LOGGER(If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat);
+void If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat::go(const shared_ptr<Shape>& element,const shared_ptr<Material>& material,const shared_ptr<Body>& bdy)
+{
+
+ shared_ptr<Lin4NodeTetra_Lin4NodeTetra_InteractionElement> interactionelement=YADE_PTR_CAST<Lin4NodeTetra_Lin4NodeTetra_InteractionElement>(element);
+ shared_ptr<LinCohesiveStiffPropDampElastMat> mat=YADE_PTR_CAST<LinCohesiveStiffPropDampElastMat>(material);
+
+
+ NodePairsMap::iterator i1(interactionelement->nodepairs.begin());
+ shared_ptr<Body> node11=i1->first.node1;shared_ptr<Body> node12=i1->first.node2;
+ Vector3r initial1=i1->second.position;
+ std::advance(i1,1);
+ shared_ptr<Body> node21= i1->first.node1;shared_ptr<Body> node22=i1->first.node2;
+ Vector3r initial2=i1->second.position;
+ std::advance(i1,1);
+ shared_ptr<Body> node31= i1->first.node1;shared_ptr<Body> node32=i1->first.node2;
+ Vector3r initial3=i1->second.position;
+
+ Vector3r disp1=(node11->state->pos-node12->state->pos)-initial1;
+ Vector3r disp2=(node21->state->pos-node22->state->pos)-initial2;
+ Vector3r disp3=(node31->state->pos-node32->state->pos)-initial3;
+
+
+
+ Vector3r l1=node11->state->pos-node21->state->pos;
+ Vector3r l2=node31->state->pos-node21->state->pos;
+
+ Real A=0.5*fabs(l1.cross(l2).norm());
+
+ Vector3r f1=(0.083333333)*A*mat->youngmodulus*(2*disp1+disp2+disp3);
+ Vector3r f2=(0.083333333)*A*mat->youngmodulus*(disp1+2*disp2+disp3);
+ Vector3r f3=(0.083333333)*A*mat->youngmodulus*(disp1+disp2+2*disp3);
+
+ //cout<<"forces are \n"<<f1<<"\n"<<f2<<"\n"<<f3<<"\n";
+
+ scene->forces.addForce(node11->getId(),-f1); scene->forces.addForce(node12->getId(),f1);
+ scene->forces.addForce(node21->getId(),-f2); scene->forces.addForce(node22->getId(),f2);
+ scene->forces.addForce(node31->getId(),-f3); scene->forces.addForce(node32->getId(),f3);
+
+
+ return;
+}
=== added file 'pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.hpp'
--- pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,39 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER burak.er@xxxxxxxxxx *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#pragma once
+#include <core/Shape.hpp>
+#include <lib/base/Math.hpp>
+#include <core/Interaction.hpp>
+#include <core/Scene.hpp>
+#include <core/State.hpp>
+#include <core/Shape.hpp>
+#include <core/IGeom.hpp>
+#include <core/IPhys.hpp>
+#include <core/Functor.hpp>
+#include <core/Dispatcher.hpp>
+#include <pkg/common/Aabb.hpp>
+#include <pkg/dem/deformablecohesive/FEInternalForceDispatchers.hpp>
+#include <pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.hpp>
+#include <pkg/dem/deformablecohesive/CohesiveMat.hpp>
+
+
+
+class If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat : public InternalForceFunctor
+{
+ public :
+
+ virtual void go(const shared_ptr<Shape>&,const shared_ptr<Material>&,const shared_ptr<Body>&);
+ virtual ~If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat();
+ FUNCTOR2D(Lin4NodeTetra_Lin4NodeTetra_InteractionElement,LinCohesiveStiffPropDampElastMat);
+
+ YADE_CLASS_BASE_DOC(If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat,InternalForceFunctor,"Apply internal forces of the tetrahedral element using lumped mass theory")
+};
+REGISTER_SERIALIZABLE(If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat);
+
+
=== added file 'pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.cpp'
--- pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,82 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER burak.er@xxxxxxxxxx *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+#include <pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.hpp>
+YADE_PLUGIN((If2_Lin4NodeTetra_LinIsoRayleighDampElast));
+If2_Lin4NodeTetra_LinIsoRayleighDampElast::~If2_Lin4NodeTetra_LinIsoRayleighDampElast(){};
+
+
+/********************************************************************
+ InternalForceDispatcher
+*********************************************************************/
+
+typedef DeformableElement::NodeMap NodeMap;
+#define VECTOR12_TEMPLATE(Scalar) Eigen::Matrix<Scalar,12,1>
+typedef VECTOR12_TEMPLATE(Real) Vector12r;
+
+CREATE_LOGGER(If2_Lin4NodeTetra_LinIsoRayleighDampElast);
+void If2_Lin4NodeTetra_LinIsoRayleighDampElast::go(const shared_ptr<Shape>& element,const shared_ptr<Material>& material,const shared_ptr<Body>& bdy)
+{
+
+ shared_ptr<Lin4NodeTetra> tetel=YADE_PTR_CAST<Lin4NodeTetra>(element);
+ shared_ptr<LinIsoRayleighDampElastMat> mat=YADE_PTR_CAST<LinIsoRayleighDampElastMat>(material);
+
+ DeformableElement::NodeMap::iterator i0(tetel->localmap.begin());
+ DeformableElement::NodeMap::iterator i1(i0);
+ DeformableElement::NodeMap::iterator i2(i0);
+ DeformableElement::NodeMap::iterator i3(i0);
+
+ std::advance(i1,1);
+ std::advance(i2,2);
+ std::advance(i3,3);
+
+ if(tetel->massMatrixInvProductstiffnessMatrix==0)
+ {
+
+ Vector3r node0relpos=Vector3r(0,0,0);
+ Vector3r node1relpos=i1->second.position-i0->second.position;
+ Vector3r node2relpos=i2->second.position-i0->second.position;
+ Vector3r node3relpos=i3->second.position-i0->second.position;
+ // I dont know wheter this is optimum or not
+ tetel->massMatrixInvProductstiffnessMatrix=shared_ptr<Matrix>
+ (
+ new Matrix(
+ tetel->calculateMassMatrix(mat->density,mat->poissonratio).inverse()*
+ tetel->calculateStiffness(mat->youngmodulus,mat->poissonratio,node0relpos,node1relpos,node2relpos,node3relpos)
+ )
+ );
+
+
+ }
+
+ //apply internal forces to the tetrahedron
+ //Calculate displacements
+ Vector12r displacements;
+ Vector12r displacementvelocity;
+
+ displacements<<i0->first->state->pos - i0->second.position,
+ i1->first->state->pos - i1->second.position,
+ i2->first->state->pos - i2->second.position,
+ i3->first->state->pos - i3->second.position;
+ displacementvelocity<<i0->first->state->vel,
+ i1->first->state->vel,
+ i2->first->state->vel,
+ i3->first->state->vel;
+
+
+ //Now calculate the forces
+ Vector12r forces=-(*tetel->massMatrixInvProductstiffnessMatrix)*displacements-(mat->alpha*Matrix::Identity(12,12)+(*tetel->massMatrixInvProductstiffnessMatrix)*(mat->beta))*displacementvelocity;
+
+ scene->forces.addForce(i0->first->getId(),forces.segment(0,3));
+ scene->forces.addForce(i1->first->getId(),forces.segment(3,3));
+ scene->forces.addForce(i2->first->getId(),forces.segment(6,3));
+ scene->forces.addForce(i3->first->getId(),forces.segment(9,3));
+
+ return;
+}
=== added file 'pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.hpp'
--- pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,39 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER burak.er@xxxxxxxxxx *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#pragma once
+#include <core/Shape.hpp>
+#include <lib/base/Math.hpp>
+#include <core/Interaction.hpp>
+#include <core/Scene.hpp>
+#include <core/State.hpp>
+#include <core/Shape.hpp>
+#include <core/IGeom.hpp>
+#include <core/IPhys.hpp>
+#include <core/Functor.hpp>
+#include <core/Dispatcher.hpp>
+#include <pkg/common/Aabb.hpp>
+#include <pkg/dem/deformablecohesive/FEInternalForceDispatchers.hpp>
+#include <pkg/dem/deformablecohesive/Lin4NodeTetra.hpp>
+#include <pkg/dem/deformablecohesive/LinElastMat.hpp>
+
+
+
+class If2_Lin4NodeTetra_LinIsoRayleighDampElast : public InternalForceFunctor
+{
+ public :
+
+ virtual void go(const shared_ptr<Shape>&,const shared_ptr<Material>&,const shared_ptr<Body>&);
+ virtual ~If2_Lin4NodeTetra_LinIsoRayleighDampElast();
+ FUNCTOR2D(Lin4NodeTetra,LinIsoRayleighDampElastMat);
+
+ YADE_CLASS_BASE_DOC(If2_Lin4NodeTetra_LinIsoRayleighDampElast,InternalForceFunctor,"Apply internal forces of the tetrahedral element using lumped mass theory")
+};
+REGISTER_SERIALIZABLE(If2_Lin4NodeTetra_LinIsoRayleighDampElast);
+
+
=== added file 'pkg/dem/deformablecohesive/Lin4NodeTetra.cpp'
--- pkg/dem/deformablecohesive/Lin4NodeTetra.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Lin4NodeTetra.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,127 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#include <pkg/dem/deformablecohesive/Lin4NodeTetra.hpp>
+#include <algorithm>
+#include <core/Scene.hpp>
+#include <core/BodyContainer.hpp>
+#include <core/State.hpp>
+#include <pkg/common/Sphere.hpp>
+#include <pkg/dem/deformablecohesive/Node.hpp>
+#include <lib/base/Math.hpp>
+
+YADE_PLUGIN((Lin4NodeTetra));
+CREATE_LOGGER(Lin4NodeTetra);
+
+Lin4NodeTetra::~Lin4NodeTetra(){
+
+}
+void Lin4NodeTetra::initialize(void){
+ maxNodeCount=4;
+}
+Matrix Lin4NodeTetra::calculateMassMatrix(Real density,Real v)
+{
+ Matrix mass(12,12);
+
+ mass<<2,0,0,1,0,0,1,0,0,1,0,0,
+ 0,2,0,0,1,0,0,1,0,0,1,0,
+ 0,0,2,0,0,1,0,0,1,0,0,1,
+ 1,0,0,2,0,0,1,0,0,1,0,0,
+ 0,1,0,0,2,0,0,1,0,0,1,0,
+ 0,0,1,0,0,2,0,0,1,0,0,1,
+ 1,0,0,1,0,0,2,0,0,1,0,0,
+ 0,1,0,0,1,0,0,2,0,0,1,0,
+ 0,0,1,0,0,1,0,0,2,0,0,1,
+ 1,0,0,1,0,0,1,0,0,2,0,0,
+ 0,1,0,0,1,0,0,1,0,0,2,0,
+ 0,0,1,0,0,1,0,0,1,0,0,2;
+
+ mass=0.05*(density*v)*mass;
+ return mass;
+}
+
+
+Matrix Lin4NodeTetra::calculateStiffness(Real E, Real v,Vector3r pos0,Vector3r pos1,Vector3r pos2,Vector3r pos3)
+{
+ /*
+ * The calculation is relative, therefore, we do not need position of the first node.
+ * All other nodes are calculated with respect to first node which is at zero on local coordinates.
+ * The local coordinates are the coordinates that is fixed at node0 and parallel to global axes.
+ *
+ * */
+
+ Vector3r pos01=-pos1;
+ Vector3r pos02=-pos2;
+ Vector3r pos03=-pos3;
+ Vector3r pos12= pos1-pos2;
+ Vector3r pos13= pos1-pos3;
+ Vector3r pos23= pos2-pos3;
+
+ Matrix J(4,4);
+
+
+
+ J.col(0)<<1,pos0;
+ J.col(1)<<1,pos1;
+ J.col(2)<<1,pos2;
+ J.col(3)<<1,pos3;
+
+
+ Real x12=pos01(0), x13=pos02(0), x14=pos03(0), x23= pos12(0), x24=pos13(0), x34= pos23(0);
+
+ Real x21=-x12, x31=-x13, x41=-x14, x32=-x23, x42=-x24, x43=-x34;
+
+ Real y12=pos01(1), y13=pos02(1), y14=pos03(1), y23= pos12(1), y24=pos13(1), y34= pos23(1);
+
+ Real y21=-y12, y31=-y13, y41=-y14, y32=-y23, y42=-y24, y43=-y34;
+
+ Real z12=pos01(2), z13=pos02(2), z14=pos03(2), z23= pos12(2), z24=pos13(2), z34= pos23(2);
+
+ Real z21=-z12, z31=-z13, z41=-z14, z32=-z23, z42=-z24, z43=-z34;
+
+ Real V=fabs(((0.166666667)*J.determinant()));
+
+
+
+ Real a1=y42*z32-y32*z42, b1=x32*z42-x42*z32, c1=x42*y32-x32*y42;
+ Real a2=y31*z43-y34*z13, b2=x43*z31-x13*z34, c2=x31*y43-x34*y13;
+ Real a3=y24*z14-y14*z24, b3=x14*z24-x24*z14, c3=x24*y14-x14*y24;
+ Real a4=y13*z21-y12*z31, b4=x21*z13-x31*z12, c4=x13*y21-x12*y31;
+
+ //std::cout<<"Volume of the element is "<<V<<"\n";
+
+ Matrix B(6,12);
+ //Construction of B matrix
+ B<<a1,0,0,a2,0,0,a3,0,0,a4,0,0,
+ 0,b1,0,0,b2,0,0,b3,0,0,b4,0,
+ 0,0,c1,0,0,c2,0,0,c3,0,0,c4,
+ b1,a1,0,b2,a2,0,b3,a3,0,b4,a4,0,
+ 0,c1,b1,0,c2,b2,0,c3,b3,0,c4,b4,
+ c1,0,a1,c2,0,a2,c3,0,a3,c4,0,a4;
+ //cout<<"B is"<<std::endl<<B<<std::endl;
+
+ B=(1/(6*V))*B;
+
+ //Construction of Elasticity matrix
+ Matrix Emtr(6,6);
+
+ Emtr<<1-v,v,v,0,0,0,
+ v,1-v,v,0,0,0,
+ v,v,1-v,0,0,0,
+ 0,0,0,0.5-v,0,0,
+ 0,0,0,0,0.5-v,0,
+ 0,0,0,0,0,0.5-v;
+
+ Emtr=E/((1+v)*(1-v))*Emtr;
+ Matrix stiffness=V*B.transpose()*Emtr*B;
+
+ return stiffness;
+
+}
+
+
+
=== added file 'pkg/dem/deformablecohesive/Lin4NodeTetra.hpp'
--- pkg/dem/deformablecohesive/Lin4NodeTetra.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Lin4NodeTetra.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,100 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#pragma once
+
+#include <core/Body.hpp>
+#include <core/PartialEngine.hpp>
+#include <pkg/dem/deformablecohesive/DeformableElement.hpp>
+#include <lib/base/Logging.hpp>
+#include <lib/base/Math.hpp>
+
+
+class NewtonIntegrator;
+
+namespace yade{
+
+#define VECTOR4_TEMPLATE(Scalar) Eigen::Matrix<Scalar,4,1>
+typedef VECTOR4_TEMPLATE(Real) Vector4r;
+
+class Lin4NodeTetra: public DeformableElement {
+ public:
+
+ friend class If2_Lin4NodeTetra_LinIsoRayleighDampElast;
+ shared_ptr<Matrix> massMatrixInvProductstiffnessMatrix;
+ Matrix calculateStiffness(Real, Real ,Vector3r,Vector3r,Vector3r,Vector3r);
+ Matrix calculateMassMatrix(Real, Real);
+ virtual ~Lin4NodeTetra();
+ void initialize(void);
+ Real getVolume(void){
+
+
+ NodeMap::iterator i0(localmap.begin());
+ NodeMap::iterator i1(i0);
+ NodeMap::iterator i2(i0);
+ NodeMap::iterator i3(i0);
+
+ std::advance(i1,1);
+ std::advance(i2,2);
+ std::advance(i3,3);
+
+ Matrix J(4,4);
+ Vector3r pos0=Vector3r(0,0,0);
+ Vector3r pos1=i1->second.position-i0->second.position;
+ Vector3r pos2=i2->second.position-i0->second.position;
+ Vector3r pos3=i3->second.position-i0->second.position;
+
+ Vector3r pos01=-pos1;
+ Vector3r pos02=-pos2;
+ Vector3r pos03=-pos3;
+ Vector3r pos12= pos1-pos2;
+ Vector3r pos13= pos1-pos3;
+ Vector3r pos23= pos2-pos3;
+
+
+ J.col(0)<<1,pos0;
+ J.col(1)<<1,pos1;
+ J.col(2)<<1,pos2;
+ J.col(3)<<1,pos3;
+
+
+ Real x12=pos01(0), x13=pos02(0), x14=pos03(0), x23= pos12(0), x24=pos13(0), x34= pos23(0);
+
+ Real x21=-x12, x31=-x13, x41=-x14, x32=-x23, x42=-x24, x43=-x34;
+
+ Real y12=pos01(1), y13=pos02(1), y14=pos03(1), y23= pos12(1), y24=pos13(1), y34= pos23(1);
+
+ Real y21=-y12, y31=-y13, y41=-y14, y32=-y23, y42=-y24, y43=-y34;
+
+ Real z12=pos01(2), z13=pos02(2), z14=pos03(2), z23= pos12(2), z24=pos13(2), z34= pos23(2);
+
+ Real z21=-z12, z31=-z13, z41=-z14, z32=-z23, z42=-z24, z43=-z34;
+
+ Real V=fabs(((0.166666667)*J.determinant()));
+
+ return V;
+ }
+
+ YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(Lin4NodeTetra,DeformableElement,"Tetrahedral Deformable Element Composed of Nodes",
+ ,
+ ,
+ createIndex(); /*ctor*/
+ initialize();
+ ,
+ /*py*/
+
+ );
+ DECLARE_LOGGER;
+
+ REGISTER_CLASS_INDEX(Lin4NodeTetra,DeformableElement);
+
+};
+}
+// necessary
+using namespace yade;
+REGISTER_SERIALIZABLE(Lin4NodeTetra);
=== added file 'pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.cpp'
--- pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,30 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#include <pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.hpp>
+#include <algorithm>
+#include <core/Scene.hpp>
+#include <core/BodyContainer.hpp>
+#include <core/State.hpp>
+#include <pkg/common/Sphere.hpp>
+#include <pkg/dem/deformablecohesive/Node.hpp>
+#include <lib/base/Math.hpp>
+
+YADE_PLUGIN((Lin4NodeTetra_Lin4NodeTetra_InteractionElement));
+CREATE_LOGGER(Lin4NodeTetra_Lin4NodeTetra_InteractionElement);
+
+Lin4NodeTetra_Lin4NodeTetra_InteractionElement::~Lin4NodeTetra_Lin4NodeTetra_InteractionElement(){
+
+}
+void Lin4NodeTetra_Lin4NodeTetra_InteractionElement::initialize(void){
+
+}
+
+
+
+
+
=== added file 'pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.hpp'
--- pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,44 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+
+#pragma once
+
+#include <map>
+#include <stdexcept>
+#include <core/Body.hpp>
+#include <lib/base/Logging.hpp>
+#include <lib/base/Math.hpp>
+#include <core/PartialEngine.hpp>
+#include <pkg/dem/deformablecohesive/DeformableCohesiveElement.hpp>
+
+
+
+class Lin4NodeTetra_Lin4NodeTetra_InteractionElement: public DeformableCohesiveElement {
+ public:
+
+ friend class If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat;
+ virtual ~Lin4NodeTetra_Lin4NodeTetra_InteractionElement();
+ void initialize(void);
+
+ YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(Lin4NodeTetra_Lin4NodeTetra_InteractionElement,DeformableCohesiveElement,"Tetrahedral Deformable Element Composed of Nodes",
+ ,
+ ,
+ createIndex(); /*ctor*/
+ initialize();
+ ,
+ /*py*/
+
+ );
+ DECLARE_LOGGER;
+
+ REGISTER_CLASS_INDEX(Lin4NodeTetra_Lin4NodeTetra_InteractionElement,DeformableCohesiveElement);
+
+};
+// necessary
+using namespace yade;
+REGISTER_SERIALIZABLE(Lin4NodeTetra_Lin4NodeTetra_InteractionElement);
=== added file 'pkg/dem/deformablecohesive/LinElastMat.cpp'
--- pkg/dem/deformablecohesive/LinElastMat.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/LinElastMat.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,14 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#include <pkg/dem/deformablecohesive/LinElastMat.hpp>
+YADE_PLUGIN((DeformableElementMaterial)(LinIsoElastMat)(LinIsoRayleighDampElastMat));
+
+DeformableElementMaterial::~DeformableElementMaterial(void){}
+LinIsoElastMat::~LinIsoElastMat(void){}
+LinIsoRayleighDampElastMat::~LinIsoRayleighDampElastMat(void){}
+
=== added file 'pkg/dem/deformablecohesive/LinElastMat.hpp'
--- pkg/dem/deformablecohesive/LinElastMat.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/LinElastMat.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,47 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#pragma once
+#include <core/Material.hpp>
+#include <limits>
+/*! Elastic material */
+class DeformableElementMaterial: public Material{
+ public:
+ virtual ~DeformableElementMaterial();
+ YADE_CLASS_BASE_DOC_ATTRS_CTOR(DeformableElementMaterial,Material,"Deformable Element Material.",
+ ((Real,density,1,,"Density of the material.")),
+ /*ctor*/ createIndex();
+ );
+ REGISTER_CLASS_INDEX(DeformableElementMaterial,Material);
+};
+REGISTER_SERIALIZABLE(DeformableElementMaterial);
+
+class LinIsoElastMat: public DeformableElementMaterial{
+ public:
+ virtual ~LinIsoElastMat();
+ YADE_CLASS_BASE_DOC_ATTRS_CTOR(LinIsoElastMat,DeformableElementMaterial,"Linear Isotropic Elastic material",
+ ((Real,youngmodulus,.78e5,,"Young's modulus. Initially aluminium."))
+ ((Real,poissonratio,.33,,"Poisson ratio. Initially aluminium.")),
+ createIndex();
+ );
+ REGISTER_CLASS_INDEX(LinIsoElastMat,DeformableElementMaterial);
+};
+REGISTER_SERIALIZABLE(LinIsoElastMat);
+
+
+/*Standard damped linear elastic material*/
+class LinIsoRayleighDampElastMat: public LinIsoElastMat{
+ public:
+ virtual ~LinIsoRayleighDampElastMat();
+ YADE_CLASS_BASE_DOC_ATTRS_CTOR(LinIsoRayleighDampElastMat,LinIsoElastMat,"Elastic material with Rayleigh Damping.",
+ ((Real,alpha,0,,"Mass propotional damping constant of Rayleigh Damping."))
+ ((Real,beta,0,,"Stiffness propotional damping constant of Rayleigh Damping.")),
+ createIndex();
+ );
+ REGISTER_CLASS_INDEX(LinIsoRayleighDampElastMat,LinIsoElastMat);
+};
+REGISTER_SERIALIZABLE(LinIsoRayleighDampElastMat);
=== added file 'pkg/dem/deformablecohesive/Node.cpp'
--- pkg/dem/deformablecohesive/Node.cpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Node.cpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,3 @@
+#include <pkg/dem/deformablecohesive/Node.hpp>
+Node::~Node(){}
+YADE_PLUGIN((Node));
=== added file 'pkg/dem/deformablecohesive/Node.hpp'
--- pkg/dem/deformablecohesive/Node.hpp 1970-01-01 00:00:00 +0000
+++ pkg/dem/deformablecohesive/Node.hpp 2016-01-07 17:49:32 +0000
@@ -0,0 +1,34 @@
+/*************************************************************************
+* Copyright (C) 2013 by Burak ER *
+* *
+* *
+* This program is free software; it is licensed under the terms of the *
+* GNU General Public License v2 or later. See file LICENSE for details. *
+*************************************************************************/
+#ifndef NODE_HPP_
+#define NODE_HPP_
+#include <core/Shape.hpp>
+//TODO: Look at Sphere hack to work around problem
+// HACK to work around https://bugs.launchpad.net/yade/+bug/528509
+// see comments there for explanation
+namespace yade{
+
+class Node: public Shape{
+ public:
+ Node(Real _radius): radius(_radius){ createIndex();}
+ virtual ~Node ();
+ YADE_CLASS_BASE_DOC_ATTRS_CTOR(Node,Shape,"Geometry of node particle.",
+ ((Real,radius,0.1,,"Radius [m]")),
+ createIndex(); /*ctor*/
+ );
+ REGISTER_CLASS_INDEX(Node,Shape);
+
+};
+
+}
+// necessary
+using namespace yade;
+
+// must be outside yade namespace
+REGISTER_SERIALIZABLE(Node);
+#endif
=== added file 'py/deformableelementsutils.py'
--- py/deformableelementsutils.py 1970-01-01 00:00:00 +0000
+++ py/deformableelementsutils.py 2016-01-07 17:49:32 +0000
@@ -0,0 +1,386 @@
+# encoding: utf-8
+#
+# utility functions for deformable cohesive elements
+#
+# burak er buraker88@xxxxxxxxxx
+
+
+import math,random,doctest,geom,numpy
+from yade import *
+from yade.wrapper import *
+from yade.utils import *
+try: # use psyco if available
+ import psyco
+ psyco.full()
+except ImportError: pass
+
+
+from minieigen import *
+
+# c++ implementations for performance reasons
+from yade._utils import *
+from yade.utils import _commonBodySetup
+
+#Deformable Element Node
+def node(center,radius,dynamic=None,fixed=True,wire=False,color=None,highlight=False,material=-1,mask=1):
+ """Create sphere with given parameters; mass and inertia computed automatically.
+
+ Last assigned material is used by default (*material* = -1), and utils.defaultMaterial() will be used if no material is defined at all.
+
+ :param Vector3 center: center
+ :param float radius: radius
+ :param float dynamic: deprecated, see "fixed"
+ :param float fixed: generate the body with all DOFs blocked?
+ :param material:
+ specify :yref:`Body.material`; different types are accepted:
+ * int: O.materials[material] will be used; as a special case, if material==-1 and there is no shared materials defined, utils.defaultMaterial() will be assigned to O.materials[0]
+ * string: label of an existing material that will be used
+ * :yref:`Material` instance: this instance will be used
+ * callable: will be called without arguments; returned Material value will be used (Material factory object, if you like)
+ :param int mask: :yref:`Body.mask` for the body
+ :param wire: display as wire sphere?
+ :param highlight: highlight this body in the viewer?
+ :param Vector3-or-None: body's color, as normalized RGB; random color will be assigned if ``None``.
+
+ :return:
+ A Body instance with desired characteristics.
+
+
+ Creating default shared material if none exists neither is given::
+
+ >>> O.reset()
+ >>> from yade import utils
+ >>> len(O.materials)
+ 0
+ >>> s0=utils.sphere([2,0,0],1)
+ >>> len(O.materials)
+ 1
+
+ Instance of material can be given::
+
+ >>> s1=utils.sphere([0,0,0],1,wire=False,color=(0,1,0),material=ElastMat(young=30e9,density=2e3))
+ >>> s1.shape.wire
+ False
+ >>> s1.shape.color
+ Vector3(0,1,0)
+ >>> s1.mat.density
+ 2000.0
+
+ Material can be given by label::
+
+ >>> O.materials.append(FrictMat(young=10e9,poisson=.11,label='myMaterial'))
+ 1
+ >>> s2=utils.sphere([0,0,2],1,material='myMaterial')
+ >>> s2.mat.label
+ 'myMaterial'
+ >>> s2.mat.poisson
+ 0.11
+
+ Finally, material can be a callable object (taking no arguments), which returns a Material instance.
+ Use this if you don't call this function directly (for instance, through yade.pack.randomDensePack), passing
+ only 1 *material* parameter, but you don't want material to be shared.
+
+ For instance, randomized material properties can be created like this:
+
+ >>> import random
+ >>> def matFactory(): return ElastMat(young=1e10*random.random(),density=1e3+1e3*random.random())
+ ...
+ >>> s3=utils.sphere([0,2,0],1,material=matFactory)
+ >>> s4=utils.sphere([1,2,0],1,material=matFactory)
+
+ """
+ b=Body()
+ b.shape=Node(radius=radius,color=color if color else randomColor(),wire=wire,highlight=highlight)
+ V=(4./3)*math.pi*radius**3
+ geomInert=(2./5.)*V*radius**2
+ _commonBodySetup(b,V,Vector3(geomInert,geomInert,geomInert),material,pos=center,dynamic=dynamic,fixed=fixed,blockedDOFs='XYZ')
+ b.aspherical=False
+ b.mask=mask
+ b.bounded=True
+ return b
+
+def randomColor():
+ """Return random Vector3 with each component in interval 0…1 (uniform distribution)"""
+ return Vector3(random.random(),random.random(),random.random())
+
+# Meshing
+def clear_mesh(gmshmeshhandle_):
+ sceneelements=gmshmeshhandle_[1];
+
+ #first remove elements and nodes from the scene
+ for elem in sceneelements:
+ bdy=elem[0];
+ nodes=elem[1];
+ O.bodies.erase(bdy.id);
+ for node in nodes:
+ O.bodies.erase(node.id);
+
+def tetrahedronvolume(nodes):
+
+
+ V =0.166666666*numpy.linalg.det([[nodes[0][0], nodes[1][0] ,nodes[2][0] ,nodes[3][0]],[nodes[0][1], nodes[1][1], nodes[2][1] ,nodes[3][1]], [nodes[0][2] ,nodes[1][2], nodes[2][2], nodes[3][2]], [ 1,1,1,1]]);
+
+ return V
+
+def tetrahedral_mesh_generator(filename,tetrahedralelementshape,elementmat,interfaceelementshape,interfacemat):
+
+
+ [nodeList,elementList,interactionList]=mshreader(filename)
+
+ nodes=nodeList
+
+ meshelements=elementList
+
+ interfacepairs=interactionList
+
+ scenebodies=[]
+
+ for elem in elementList:
+ #Create the corresponding mesh element
+ nodesofelement=[nodes[elem[0]],nodes[elem[1]],nodes[elem[2]],nodes[elem[3]]]
+ noderadius=0.1*(0.75*tetrahedronvolume(nodesofelement))**0.33333333;
+
+ [elbody, nodebodies]=tetrahedral_element(elementmat,nodesofelement,tetrahedralelementshape,radius=noderadius)
+
+ scenebodies.append([elbody,nodebodies])
+
+ #Create the interfacing element pairs
+ for interpair in interfacepairs:
+
+ #get element pair
+ elementpair=interpair[0];
+ #get node pairs
+ pairofnodes=interpair[1]
+ interfaceelementpairs=[]
+
+ for pair in pairofnodes:
+
+ firstid=pair[0];
+ secondid=pair[1];
+ el1nodebodies=scenebodies[elementpair[0]][1];
+ el2nodebodies=scenebodies[elementpair[1]][1];
+ node1=el1nodebodies[firstid]
+ node2=el2nodebodies[secondid]
+ interfaceelementpairs.append([node1, node2])
+
+ [elbody, nodebodies]=interaction_element(interfacemat,interfaceelementpairs,interfaceelementshape);
+ scenebodies.append([elbody,nodebodies])
+
+ return scenebodies
+
+
+#Read mesh file and get elements nodes and interactions
+def mshreader(meshfile="file.mesh",shift=Vector3.Zero,scale=1.0,orientation=Quaternion.Identity,**kw):
+ """ Imports volume mesh from gmsh2 file
+ :Parameters:
+ `shift`: [float,float,float]
+ [X,Y,Z] parameter moves the specimen.
+ `scale`: float
+ factor scales the given data.
+ `orientation`: quaternion
+ orientation of the imported mesh
+ `**kw`: (unused keyword arguments)
+ is passed to :yref:`yade.utils.facet`
+ :Returns: list of nodes and elements for the specimen.
+ """
+ infile = open(meshfile,"r")
+ lines = infile.readlines()
+ infile.close()
+
+ nodelistVector3=[]
+ elementList=[]
+ interactionList=[]
+ findVerticesString=0
+
+ while (lines[findVerticesString].split()[0]<>'$Nodes'): #Find the string with the number of Vertices
+ findVerticesString+=1
+ findVerticesString+=1
+ numNodes = int(lines[findVerticesString].split()[0])
+
+ for line in lines[findVerticesString+1:numNodes+findVerticesString+1]:
+ data = line.split()
+ nodelistVector3.append(orientation*Vector3(float(data[1])*scale,float(data[2])*scale,float(data[3])*scale)+shift)
+
+ findElementString=findVerticesString+numNodes
+ while (lines[findElementString].split()[0]<>'$Elements'): #Find the string with the number of Elements
+ findElementString+=1
+ findElementString+=1
+ numElements = int(lines[findElementString].split()[0])
+
+
+ for line in lines[findElementString+1:findElementString+numElements+1]:
+ data = line.split()
+ numberofnodes=data[1]
+
+ if(int(numberofnodes)==4):#tetrahedral element
+
+ id1 = int(data[5])-1
+ id2 = int(data[6])-1
+ id3 = int(data[7])-1
+ id4 = int(data[8])-1
+ elementList.append([id1,id2,id3,id4])
+ #Create the interaction list
+ i=0
+ numVolElements=elementList.__len__()
+ for elem in elementList:
+ j=i+1
+
+ while j<numVolElements :
+
+ pair=check_coinciding_nodes(elem,elementList[j])
+ if(pair.__len__()>0):
+ interactionList.append([Vector2i(i,j),pair])
+ j=j+1
+ i=i+1
+ return [nodelistVector3,elementList,interactionList]
+
+def check_coinciding_nodes(element1,element2):
+
+ pairstemp=[]
+ #for each node of the element1
+ i=0
+ j=0
+ for node1 in element1:
+
+ for node2 in element2:
+
+ if(node1==node2):
+ pairstemp.append([i,j])
+ j=j+1
+ i=i+1
+ j=0
+ if(3<=pairstemp.__len__()):
+ pairs=pairstemp
+ else:
+ pairs=[]
+ return pairs
+
+def interaction_element(material,nodepairs,elementshape,radius=0.0015,dynamic=None,fixed=True,wire=False,color=Vector3(1,0,0),highlight=False,mask=1):
+
+ # triangles for drawing(node indices)
+ #faces=[Vector3(0,1,3),Vector3(1,2,3),Vector3(2,0,3),Vector3(0,1,2)]
+ faces=[];
+ shape=elementshape()
+ shape.color=color if color else randomColor();
+ [body_,nodes_]=finite_element(material,shape,nodepairs,faces,radius,interface=True)
+
+ return [body_,nodes_]
+
+def tetrahedral_element(material,nodes,elementshape,radius=0.0015,dynamic=None,fixed=True,wire=False,color=Vector3(1,0,0),highlight=False,mask=1):
+
+ # triangles for drawing(node indices)
+ #faces are in the format [face_vertex0,face_vertex1,face_vertex2,opposite_vertex]
+ faces=[Vector3(1,2,0),Vector3(2,1,3),Vector3(2,0,3),Vector3(3,1,0)]
+
+ shape=elementshape()
+ shape.color=color if color else randomColor();
+ [body_,nodes_]=finite_element(material,shape,nodes,faces,radius)
+
+ return [body_,nodes_]
+
+def finite_element(material,shape,nodes,faces,radius,dynamic=None,fixed=True,wire=False,Color=None,highlight=False,mask=1,interface=False):
+ """Create sphere with given parameters; mass and inertia computed automatically.
+
+ Last assigned material is used by default (*material* = -1), and utils.defaultMaterial() will be used if no material is defined at all.
+
+ :param Vector3 center: center
+ :param float radius: radius
+ :param float dynamic: deprecated, see "fixed"
+ :param float fixed: generate the body with all DOFs blocked?
+ :param material:
+ specify :yref:`Body.material`; different types are accepted:
+ * int: O.materials[material] will be used; as a special case, if material==-1 and there is no shared materials defined, utils.defaultMaterial() will be assigned to O.materials[0]
+ * string: label of an existing material that will be used
+ * :yref:`Material` instance: this instance will be used
+ * callable: will be called without arguments; returned Material value will be used (Material factory object, if you like)
+ :param int mask: :yref:`Body.mask` for the body
+ :param wire: display as wire sphere?
+ :param highlight: highlight this body in the viewer?
+ :param Vector3-or-None: body's color, as normalized RGB; random color will be assigned if ``None``.
+
+ :return:
+ A Body instance with desired characteristics.
+
+
+ Creating default shared material if none exists neither is given::
+
+ >>> O.reset()
+ >>> from yade import utils
+ >>> len(O.materials)
+ 0
+ >>> s0=utils.sphere([2,0,0],1)
+ >>> len(O.materials)
+ 1
+
+ Instance of material can be given::
+
+ >>> s1=utils.sphere([0,0,0],1,wire=False,color=(0,1,0),material=ElastMat(young=30e9,density=2e3))
+ >>> s1.shape.wire
+ False
+ >>> s1.shape.color
+ Vector3(0,1,0)
+ >>> s1.mat.density
+ 2000.0
+
+ Material can be given by label::
+
+ >>> O.materials.append(FrictMat(young=10e9,poisson=.11,label='myMaterial'))
+ 1
+ >>> s2=utils.sphere([0,0,2],1,material='myMaterial')
+ >>> s2.mat.label
+ 'myMaterial'
+ >>> s2.mat.poisson
+ 0.11
+
+ Finally, material can be a callable object (taking no arguments), which returns a Material instance.
+ Use this if you don't call this function directly (for instance, through yade.pack.randomDensePack), passing
+ only 1 *material* parameter, but you don't want material to be shared.
+
+ For instance, randomized material properties can be created like this:
+
+ >>> import random
+ >>> def matFactory(): return ElastMat(young=1e10*random.random(),density=1e3+1e3*random.random())
+ ...
+ >>> s3=utils.sphere([0,2,0],1,material=matFactory)
+ >>> s4=utils.sphere([1,2,0],1,material=matFactory)
+
+ """
+ b=Body();
+ b.shape=shape;
+ O.bodies.append(b)
+ nodes_ret=[];
+ #b.shape.color=Color;
+ #add nodes to the scene and keep them in the nodes list
+ if(interface==False):
+ #Deformable Element
+ for vec in nodes: # Second Example
+ nod=node(vec,radius)
+ O.bodies.append(nod)
+ b.shape.addNode(nod)
+ nodes_ret.append(nod)
+ #add faces for drawing purposes
+ for face in faces:
+ b.shape.addFace(face)
+ else:
+ #Deformable Cohesive Element
+ for nodepair in nodes: # Second Example
+ b.shape.addPair(nodepair[0],nodepair[1])
+ #add faces for drawing purposes
+ for face in faces:
+ b.shape.addFace(face)
+
+ V=1;#For symbolical
+ geomInert=Vector3(1,1,1)#For symbolical
+ #Only add body to draw it not for integration, therefore block all dof
+ _commonBodySetup(b,V,geomInert,material,pos=Vector3(0,0,0),dynamic=False,fixed=True,blockedDOFs='xyzXYZ')
+ b.aspherical=False
+ b.mask=mask
+ b.bounded=False
+ return [b,nodes_ret]
+
+
+
+
+
+##**********************End of Deformable Elements*********************************
+
=== modified file 'py/utils.py'
--- py/utils.py 2015-12-10 12:18:07 +0000
+++ py/utils.py 2016-01-07 17:49:32 +0000
@@ -110,7 +110,7 @@
"""
return FrictMat(density=1e3,young=1e7,poisson=.3,frictionAngle=.5,label='defaultMat')
-def _commonBodySetup(b,volume,geomInertia,material,pos,noBound=False,resetState=True,dynamic=None,fixed=False):
+def _commonBodySetup(b,volume,geomInertia,material,pos,noBound=False,resetState=True,dynamic=None,fixed=False,blockedDOFs='xyzXYZ'):
"""Assign common body parameters."""
if isinstance(material,int):
if material<0 and len(O.materials)==0: O.materials.append(defaultMaterial());
@@ -129,7 +129,7 @@
import warnings
warnings.warn('dynamic=%s is deprecated, use fixed=%s instead'%(str(dynamic),str(not dynamic)),category=DeprecationWarning,stacklevel=2)
fixed=not dynamic
- b.state.blockedDOFs=('xyzXYZ' if fixed else '')
+ b.state.blockedDOFs=(blockedDOFs if fixed else '')
def sphere(center,radius,dynamic=None,fixed=False,wire=False,color=None,highlight=False,material=-1,mask=1):
=== modified file 'py/ymport.py'
--- py/ymport.py 2015-12-09 00:21:24 +0000
+++ py/ymport.py 2016-01-07 17:49:32 +0000
@@ -165,6 +165,7 @@
infile.close()
nodelistVector3=[]
+ elementlistVector3=[] # for deformable elements
findVerticesString=0
while (lines[findVerticesString].split()[0]<>'Vertices'): #Find the string with the number of Vertices
