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  3. Message #06755

[Branch ~yade-dev/yade/trunk] Rev 2666: 1. Unbreak the periodic cell.

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------------------------------------------------------------
revno: 2666
committer: Václav Šmilauer <eu@xxxxxxxx>
branch nick: yade
timestamp: Thu 2011-01-20 15:55:15 +0100
message:
  1. Unbreak the periodic cell.
added:
  py/tests/engines.py
renamed:
  py/tests/omega.py => py/tests/core.py
modified:
  core/Cell.cpp
  core/Cell.hpp
  core/Scene.cpp
  examples/concrete/periodic.py
  py/pack/pack.py
  py/tests/__init__.py
  py/tests/pbc.py
  py/tests/wrapper.py
  scripts/test/facet-sphere-ViscElBasic-peri.py
  scripts/test/peri3dController_example1.py
  scripts/test/peri3dController_shear.py
  scripts/test/peri8.py
  scripts/test/periodic-compress.py
  scripts/test/periodic-geom-compare.py
  scripts/test/periodic-grow.py
  scripts/test/periodic-shear.py
  scripts/test/periodic-simple-shear.py
  scripts/test/periodic-simple.py
  scripts/test/periodic-triax.py
  scripts/test/sphere-sphere-ViscElBasic-peri.py
  py/tests/core.py


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=== modified file 'core/Cell.cpp'
--- core/Cell.cpp	2011-01-19 18:47:05 +0000
+++ core/Cell.cpp	2011-01-20 14:55:15 +0000
@@ -9,6 +9,7 @@
 	invTrsf=trsf.inverse();
 	// Hsize contains colums with updated base vectors
 	Hsize+=_trsfInc*Hsize;
+	if(Hsize.determinant()==0){ throw runtime_error("Cell is degenerate (zero volume)."); }
 	// lengths of transformed cell vectors, skew cosines
 	Matrix3r Hnorm; // normalized transformed base vectors
 	for(int i=0; i<3; i++){

=== modified file 'core/Cell.hpp'
--- core/Cell.hpp	2011-01-19 18:47:05 +0000
+++ core/Cell.hpp	2011-01-20 14:55:15 +0000
@@ -88,10 +88,15 @@
 	Vector3r bodyFluctuationVel(const Vector3r& pos, const Vector3r& vel) const { if(homoDeform==HOMO_VEL || homoDeform==HOMO_VEL_2ND) return (vel-velGrad*pos); return vel; }
 
 	Vector3r getRefSize() const { return refSize; }
-	void setRefSize(const Vector3r& s){refSize=s; Hsize=Matrix3r::Zero(); Hsize.diagonal()=refSize; Hsize=trsf*Hsize; integrateAndUpdate(0);}
-	void setInitHsize(const Matrix3r& m){Hsize=m; for (int k=0;k<3;k++) refSize[k]=Hsize.col(k).norm(); integrateAndUpdate(0);}
+	// change length of initial cell vectors (scale current Hsize by the ratio)
+	// should be identical to: { refSize=s; Hsize=invTrsf*Hsize; for(int i=0;i<3;i++) Hsize.col(i)=Hsize.col(i).normalized()*refSize[i]; /* transform back*/ Hsize=trsf*Hsize; integrateAndUpdate(0); }
+	void setRefSize(const Vector3r& s){ for(int i=0;i<3;i++) Hsize.col(i)*=s[i]/refSize[i]; refSize=s; integrateAndUpdate(0); } 
+	Matrix3r getHsize() const { return Hsize; }
+	void setHsize(const Matrix3r& m){ Hsize=m; for(int k=0;k<3;k++) refSize[k]=Hsize.col(k).norm(); integrateAndUpdate(0);}
+	Matrix3r getHsize0() const { return invTrsf*Hsize; }
 	Matrix3r getTrsf() const { return trsf; }
 	void setTrsf(const Matrix3r& m){ Hsize=m*invTrsf*Hsize; trsf=m; integrateAndUpdate(0); }
+
 	// return current cell volume
 	Real getVolume() const {return Hsize.determinant();}
 	void postLoad(Cell&){ integrateAndUpdate(0); }
@@ -103,15 +108,23 @@
 	enum { HOMO_NONE=0, HOMO_POS=1, HOMO_VEL=2, HOMO_VEL_2ND=3 };
 	
 	YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Cell,Serializable,"Parameters of periodic boundary conditions. Only applies if O.isPeriodic==True.",
-		((Vector3r,refSize,Vector3r(1,1,1),Attr::readonly,"Reference size of the cell. Change the value with :yref:`Cell::setRefSize`"))
-		((Matrix3r,trsf,Matrix3r::Identity(),Attr::readonly,"Current transformation matrix of the cell. Change the value with :yref:`Cell::setTrsf`"))
+		/* overridden below to be modified by getters/setters because of intended side-effects */
+		((Vector3r,refSize,Vector3r(1,1,1),,"[overridden]"))
+		((Matrix3r,trsf,Matrix3r::Identity(),,"[overridden]"))
+		((Matrix3r,Hsize,Matrix3r::Identity(),,"[overridden]"))
+		/* normal attributes */
 		((Matrix3r,invTrsf,Matrix3r::Identity(),Attr::readonly,"Inverse of current transformation matrix of the cell."))
-		((Matrix3r,velGrad,Matrix3r::Zero(),,"Velocity gradient of the transformation; used in NewtonIntegrator."))
+		((Matrix3r,velGrad,Matrix3r::Zero(),,"Velocity gradient of the transformation; used in :yref:`NewtonIntegrator`."))
 		((Matrix3r,prevVelGrad,Matrix3r::Zero(),Attr::readonly,"Velocity gradient in the previous step."))
-		((Matrix3r,Hsize,Matrix3r::Zero(),Attr::readonly,"The current cell size (one column per box edge), computed from *refSize* and *trsf* |yupdate|"))
 		((int,homoDeform,3,Attr::triggerPostLoad,"Deform (:yref:`velGrad<Cell.velGrad>`) the cell homothetically, by adjusting positions or velocities of particles. The values have the following meaning: 0: no homothetic deformation, 1: set absolute particle positions directly (when ``velGrad`` is non-zero), but without changing their velocity, 2: adjust particle velocity (only when ``velGrad`` changed) with Δv_i=Δ ∇v x_i. 3: as 2, but include a 2nd order term in addition -- the derivative of 1 (convective term in the velocity update).")),
 		/*ctor*/ integrateAndUpdate(0),
 		/*py*/
+		// override some attributes above
+		.add_property("refSize",&Cell::getRefSize,&Cell::setRefSize,"Reference size of the cell (lengths of initial cell vectors, i.e. columns of :yref:`Hsize<Cell.Hsize>`). Modifying this value will scale cell vectors such to have desired length.")
+		.add_property("Hsize",&Cell::getHsize,&Cell::setHsize,"Base cell vectors (columns of the matrix), updated at every step from :yref:`velGrad<Cell.velGrad>` (:yref:`trsf<Cell.trsf>` accumulates applied :yref:`velGrad<Cell.velGrad>` transformations).")
+		.add_property("trsf",&Cell::getTrsf,&Cell::setTrsf,"Current transformation matrix of the cell.")
+		// useful properties
+		.add_property("Hsize0",&Cell::getHsize0,"Initial value of Hsize, before applying transformation (computed as :yref:`invTrsf<Cell.invTrsf>` × :yref:`Hsize<Cell.Hsize>`.")
 		.def_readonly("size",&Cell::getSize_copy,"Current size of the cell, i.e. lengths of 3 cell lateral vectors after applying current trsf. Update automatically at every step.")
 		.add_property("volume",&Cell::getVolume,"Current volume of the cell.")
 		// debugging only
@@ -119,9 +132,6 @@
 		.def("unshearPt",&Cell::unshearPt,"Apply inverse shear on the point (removes skew+rot of the cell)")
 		.def("shearPt",&Cell::shearPt,"Apply shear (cell skew+rot) on the point")
 		.def("wrapPt",&Cell::wrapPt_py,"Wrap point inside the reference cell, assuming the cell has no skew+rot.")
-		.def("setTrsf",&Cell::setTrsf,"Set transformation (will update Hsize as if it was initialy an axis-aligned cuboïd).")
-		.def("setRefSize",&Cell::setRefSize,"Set reference size of the cell (will update Hsize as if the cell was initialy an axis-aligned cuboïd).")
-		.def("setInitHsize",&Cell::setInitHsize,"Define reference base vectors of the undeformed period. The shape is arbitrary: a non-rectangular parallepiped can be defined as the reference configuration, and will correspond to trsf=0.")
 		.def_readonly("shearTrsf",&Cell::_shearTrsf,"Current skew+rot transformation (no resize)")
 		.def_readonly("unshearTrsf",&Cell::_unshearTrsf,"Inverse of the current skew+rot transformation (no resize)")
 	);

=== modified file 'core/Scene.cpp'
--- core/Scene.cpp	2010-11-24 22:42:15 +0000
+++ core/Scene.cpp	2011-01-20 14:55:15 +0000
@@ -27,6 +27,7 @@
 #include<unistd.h>
 #include<time.h>
 
+namespace py=boost::python;
 
 YADE_PLUGIN((Scene));
 CREATE_LOGGER(Scene);
@@ -49,6 +50,7 @@
 	tags.push_back("id="+id);
 	tags.push_back("d.id="+id);
 	tags.push_back("id.d="+id);
+	// tags.push_back("revision="+py::extract<string>(py::import("yade.config").attr("revision"))());;
 }
 
 

=== modified file 'examples/concrete/periodic.py'
--- examples/concrete/periodic.py	2011-01-19 18:22:56 +0000
+++ examples/concrete/periodic.py	2011-01-20 14:55:15 +0000
@@ -82,7 +82,7 @@
 avgRadius=numpy.average([r for c,r in sp])
 O.bodies.append([utils.sphere(c,r,color=utils.randomColor()) for c,r in sp])
 O.periodic=True
-O.cell.setRefSize(sp.cellSize)
+O.cell.refSize=sp.cellSize
 axis=2
 ax1=(axis+1)%3
 ax2=(axis+2)%3

=== modified file 'py/pack/pack.py'
--- py/pack/pack.py	2011-01-19 18:22:56 +0000
+++ py/pack/pack.py	2011-01-20 14:55:15 +0000
@@ -90,8 +90,8 @@
 	assert(isinstance(rot,Matrix3))
 	if self.cellSize!=Vector3.Zero:
 		O.periodic=True
-		O.cell.setTrsf(rot)
-		O.cell.setRefSize(self.cellSize)
+		O.cell.trsf=rot
+		O.cell.refSize=self.cellSize
 	if not self.hasClumps():
 		return O.bodies.append([utils.sphere(rot*c,r,**kw) for c,r in self])
 	else:
@@ -427,12 +427,12 @@
 		# x1,y1,z1 already computed above
 		sp=SpherePack()
 		O.periodic=True
-		O.cell.setRefSize(Vector3(x1,y1,z1))
+		O.cell.refSize=(x1,y1,z1)
 		#print cloudPorosity,beta,gamma,N100,x1,y1,z1,O.cell.refSize
 		#print x1,y1,z1,radius,rRelFuzz
 		O.materials.append(FrictMat(young=3e10,density=2400))
 		num=sp.makeCloud(Vector3().Zero,O.cell.refSize,radius,rRelFuzz,spheresInCell,True)
-		O.engines=[ForceResetter(),InsertionSortCollider([Bo1_Sphere_Aabb()],nBins=5,sweepLength=.05*radius),InteractionLoop([Ig2_Sphere_Sphere_Dem3DofGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_Dem3DofGeom_FrictPhys_CundallStrack()]),PeriIsoCompressor(charLen=2*radius,stresses=[-100e9,-1e8],maxUnbalanced=1e-2,doneHook='O.pause();',globalUpdateInt=5,keepProportions=True),NewtonIntegrator(damping=.6)]
+		O.engines=[ForceResetter(),InsertionSortCollider([Bo1_Sphere_Aabb()],nBins=5,verletDist=.05*radius),InteractionLoop([Ig2_Sphere_Sphere_Dem3DofGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_Dem3DofGeom_FrictPhys_CundallStrack()]),PeriIsoCompressor(charLen=2*radius,stresses=[-100e9,-1e8],maxUnbalanced=1e-2,doneHook='O.pause();',globalUpdateInt=5,keepProportions=True),NewtonIntegrator(damping=.6)]
 		O.materials.append(FrictMat(young=30e9,frictionAngle=.5,poisson=.3,density=1e3))
 		for s in sp: O.bodies.append(utils.sphere(s[0],s[1]))
 		O.dt=utils.PWaveTimeStep()
@@ -478,9 +478,9 @@
 	O.switchScene(); O.resetThisScene()
 	sp=SpherePack()
 	O.periodic=True
-	O.cell.setRefSize(Vector3(initSize))
+	O.cell.refSize=initSize
 	sp.makeCloud(Vector3().Zero,O.cell.refSize,radius,rRelFuzz,-1,True)
-	O.engines=[ForceResetter(),InsertionSortCollider([Bo1_Sphere_Aabb()],nBins=2,sweepLength=.05*radius),InteractionLoop([Ig2_Sphere_Sphere_Dem3DofGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_Dem3DofGeom_FrictPhys_CundallStrack()]),PeriIsoCompressor(charLen=2*radius,stresses=[-100e9,-1e8],maxUnbalanced=1e-2,doneHook='O.pause();',globalUpdateInt=20,keepProportions=True),NewtonIntegrator(damping=.8)]
+	O.engines=[ForceResetter(),InsertionSortCollider([Bo1_Sphere_Aabb()],nBins=2,verletDist=.05*radius),InteractionLoop([Ig2_Sphere_Sphere_Dem3DofGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_Dem3DofGeom_FrictPhys_CundallStrack()]),PeriIsoCompressor(charLen=2*radius,stresses=[-100e9,-1e8],maxUnbalanced=1e-2,doneHook='O.pause();',globalUpdateInt=20,keepProportions=True),NewtonIntegrator(damping=.8)]
 	O.materials.append(FrictMat(young=30e9,frictionAngle=.1,poisson=.3,density=1e3))
 	for s in sp: O.bodies.append(utils.sphere(s[0],s[1]))
 	O.dt=utils.PWaveTimeStep()

=== modified file 'py/tests/__init__.py'
--- py/tests/__init__.py	2011-01-12 16:22:18 +0000
+++ py/tests/__init__.py	2011-01-20 14:55:15 +0000
@@ -4,7 +4,7 @@
 import unittest,inspect
 
 # add any new test suites to the list here, so that they are picked up by testAll
-allTests=['wrapper','omega','pbc','clump','cohesive-chain']
+allTests=['wrapper','core','pbc','clump','cohesive-chain']
 
 # all yade modules (ugly...)
 import yade.eudoxos,yade.export,yade.linterpolation,yade.log,yade.pack,yade.plot,yade.post2d,yade.timing,yade.utils,yade.ymport,yade.geom

=== renamed file 'py/tests/omega.py' => 'py/tests/core.py'
--- py/tests/omega.py	2011-01-19 18:22:56 +0000
+++ py/tests/core.py	2011-01-20 14:55:15 +0000
@@ -2,7 +2,7 @@
 # 2009 © Václav Šmilauer <eudoxos@xxxxxxxx>
 
 """
-Basic functionality of Omega, such as accessing bodies, materials, interactions.
+Core functionality (Scene in c++), such as accessing bodies, materials, interactions. Specific functionality tests should go to engines.py or elsewhere, not here.
 """
 import unittest
 import random
@@ -18,10 +18,10 @@
 class TestForce(unittest.TestCase): pass
 class TestTags(unittest.TestCase): pass 
 
-class TestEngines(unittest.TestCase):
+class TestLoop(unittest.TestCase):
 	def setUp(self): O.reset()
 	def testSubstepping(self):
-		'Engines: substepping'
+		'Loop: substepping'
 		O.engines=[ForceResetter(),PyRunner(initRun=True,iterPeriod=1,command='pass'),GravityEngine()]
 		# value outside the loop
 		self.assert_(O.subStep==-1)
@@ -36,7 +36,7 @@
 		O.engines=[PyRunner(initRun=True,iterPeriod=1,command='if O.subStep!=0: raise RuntimeError("O.subStep!=0 inside the loop with O.subStepping==False!")')]
 		O.step()
 	def testEnginesModificationInsideLoop(self):
-		'Engines: can be modified inside the loop transparently.'
+		'Loop: O.engines can be modified inside the loop transparently.'
 		O.engines=[
 			PyRunner(initRun=True,iterPeriod=1,command='from yade import *; O.engines=[ForceResetter(),GravityEngine(),NewtonIntegrator()]'), # change engines here
 			ForceResetter() # useless engine
@@ -56,54 +56,9 @@
 		self.assert_(len(O.engines)==3)
 		self.assert_(len(O._currEngines)==3)
 	def testDead(self):
-		'Engines: dead engines are not run'
+		'Loop: dead engines are not run'
 		O.engines=[PyRunner(dead=True,initRun=True,iterPeriod=1,command='pass')]
 		O.step(); self.assert_(O.engines[0].nDone==0)
-	def testKinematicEngines(self):
-		'Engines: test kinematic engines'
-		tolerance = 1e-5
-		rotIndex=1.0
-		angVelTemp = pi/rotIndex
-		O.reset()
-		id_fixed_transl = O.bodies.append(utils.sphere((0.0,0.0,0.0),1.0,fixed=True))
-		id_nonfixed_transl = O.bodies.append(utils.sphere((0.0,5.0,0.0),1.0,fixed=False))
-		id_fixed_rot = O.bodies.append(utils.sphere((0.0,10.0,10.0),1.0,fixed=True))
-		id_nonfixed_rot = O.bodies.append(utils.sphere((0.0,15.0,10.0),1.0,fixed=False))
-		id_fixed_helix = O.bodies.append(utils.sphere((0.0,20.0,10.0),1.0,fixed=True))
-		id_nonfixed_helix = O.bodies.append(utils.sphere((0.0,25.0,10.0),1.0,fixed=False))
-		O.engines=[
-			
-			TranslationEngine(velocity = 1.0, translationAxis = [1.0,0,0], ids = [id_fixed_transl]),
-			TranslationEngine(velocity = 1.0, translationAxis = [1.0,0,0], ids = [id_nonfixed_transl]),
-			RotationEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], rotateAroundZero = True, zeroPoint = [0.0,0.0,0.0], ids = [id_fixed_rot]),
-			RotationEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], rotateAroundZero = True, zeroPoint = [0.0,5.0,0.0], ids = [id_nonfixed_rot]),
-			HelixEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], linearVelocity = 1.0, zeroPoint = [0.0,0.0,0.0], ids = [id_fixed_helix]),
-			HelixEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], linearVelocity = 1.0, zeroPoint = [0.0,5.0,0.0], ids = [id_nonfixed_helix]),
-			ForceResetter(),
-			NewtonIntegrator()
-		]
-		O.dt = 1.0
-		for i in range(0,25):
-			O.step()
-			self.assertTrue(abs(O.bodies[id_fixed_transl].state.pos[0] - O.iter) < tolerance)												#Check translation of fixed bodies
-			self.assertTrue(abs(O.bodies[id_nonfixed_transl].state.pos[0] - O.iter) < tolerance)										#Check translation of nonfixed bodies
-			
-			self.assertTrue(abs(O.bodies[id_fixed_rot].state.pos[0]-10.0*sin(pi/angVelTemp*O.iter))<tolerance)			#Check rotation of fixed bodies X
-			self.assertTrue(abs(O.bodies[id_fixed_rot].state.pos[2]-10.0*cos(pi/angVelTemp*O.iter))<tolerance)			#Check rotation of fixed bodies Y
-			self.assertTrue(abs(O.bodies[id_fixed_rot].state.ori.toAxisAngle()[1]-Quaternion(Vector3(0.0,1.0,0.0),pi/angVelTemp*O.iter).toAxisAngle()[1])<tolerance)		#Check rotation of fixed bodies, angle
-			
-			self.assertTrue(abs(O.bodies[id_nonfixed_rot].state.pos[0] - 10*sin(pi/angVelTemp*O.iter))<tolerance)		#Check rotation of nonfixed bodies X
-			self.assertTrue(abs(O.bodies[id_nonfixed_rot].state.pos[2] - 10*cos(pi/angVelTemp*O.iter))<tolerance)		#Check rotation of nonfixed bodies Y
-			self.assertTrue(abs(O.bodies[id_nonfixed_rot].state.ori.toAxisAngle()[1]-Quaternion(Vector3(0.0,1.0,0.0),pi/angVelTemp*O.iter).toAxisAngle()[1])<tolerance)		#Check rotation of nonfixed bodies, angle
-						
-			self.assertTrue(abs(O.bodies[id_fixed_helix].state.pos[0] - 10*sin(pi/angVelTemp*O.iter))<tolerance)		#Check helixEngine of fixed bodies X
-			self.assertTrue(abs(O.bodies[id_fixed_helix].state.pos[2] - 10*cos(pi/angVelTemp*O.iter))<tolerance)		#Check helixEngine of fixed bodies Y
-			self.assertTrue(abs(O.bodies[id_fixed_helix].state.pos[1]-20.0 - O.iter)<tolerance)		#Check helixEngine of fixed bodies Z
-			
-			self.assertTrue(abs(O.bodies[id_nonfixed_helix].state.pos[0] - 10*sin(pi/angVelTemp*O.iter))<tolerance)		#Check helixEngine of nonfixed bodies X
-			self.assertTrue(abs(O.bodies[id_nonfixed_helix].state.pos[2] - 10*cos(pi/angVelTemp*O.iter))<tolerance)		#Check helixEngine of nonfixed bodies Y
-			self.assertTrue(abs(O.bodies[id_nonfixed_helix].state.pos[1]-25.0 - O.iter)<tolerance)		#Check helixEngine of nonfixed bodies Z
-
 			
 
 
@@ -123,15 +78,6 @@
 		failed=list(failed); failed.sort()
 		self.assert_(len(failed)==0,'Failed classes were: '+' '.join(failed))
 
-
-class TestCell(unittest.TestCase):
-	def setUp(self):
-		O.reset(); O.periodic=True
-	def testAttributesAreCrossUpdated(self):
-		"Cell: updates Hsize automatically when refSize is updated"
-		O.cell.setRefSize((2.55,11,45))
-		self.assert_(O.cell.Hsize==Matrix3(2.55,0,0, 0,11,0, 0,0,45));
-
 class TestMaterialStateAssociativity(unittest.TestCase):
 	def setUp(self): O.reset()
 	def testThrowsAtBadCombination(self):

=== added file 'py/tests/engines.py'
--- py/tests/engines.py	1970-01-01 00:00:00 +0000
+++ py/tests/engines.py	2011-01-20 14:55:15 +0000
@@ -0,0 +1,58 @@
+'test functionality of individual engines'
+
+import unittest
+import random
+from yade.wrapper import *
+from miniEigen import *
+from yade._customConverters import *
+from yade import utils
+from yade import *
+from math import *
+
+
+class TestKinematicEngines(unittest.TestCase):
+	def testKinematicEngines(self):
+		'Engines: kinematic engines'
+		tolerance = 1e-5
+		rotIndex=1.0
+		angVelTemp = pi/rotIndex
+		O.reset()
+		id_fixed_transl = O.bodies.append(utils.sphere((0.0,0.0,0.0),1.0,fixed=True))
+		id_nonfixed_transl = O.bodies.append(utils.sphere((0.0,5.0,0.0),1.0,fixed=False))
+		id_fixed_rot = O.bodies.append(utils.sphere((0.0,10.0,10.0),1.0,fixed=True))
+		id_nonfixed_rot = O.bodies.append(utils.sphere((0.0,15.0,10.0),1.0,fixed=False))
+		id_fixed_helix = O.bodies.append(utils.sphere((0.0,20.0,10.0),1.0,fixed=True))
+		id_nonfixed_helix = O.bodies.append(utils.sphere((0.0,25.0,10.0),1.0,fixed=False))
+		O.engines=[
+			TranslationEngine(velocity = 1.0, translationAxis = [1.0,0,0], ids = [id_fixed_transl]),
+			TranslationEngine(velocity = 1.0, translationAxis = [1.0,0,0], ids = [id_nonfixed_transl]),
+			RotationEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], rotateAroundZero = True, zeroPoint = [0.0,0.0,0.0], ids = [id_fixed_rot]),
+			RotationEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], rotateAroundZero = True, zeroPoint = [0.0,5.0,0.0], ids = [id_nonfixed_rot]),
+			HelixEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], linearVelocity = 1.0, zeroPoint = [0.0,0.0,0.0], ids = [id_fixed_helix]),
+			HelixEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], linearVelocity = 1.0, zeroPoint = [0.0,5.0,0.0], ids = [id_nonfixed_helix]),
+			ForceResetter(),
+			NewtonIntegrator()
+		]
+		O.dt = 1.0
+		for i in range(0,2):
+			O.step()
+			self.assertTrue(abs(O.bodies[id_fixed_transl].state.pos[0] - O.iter) < tolerance)												#Check translation of fixed bodies
+			self.assertTrue(abs(O.bodies[id_nonfixed_transl].state.pos[0] - O.iter) < tolerance)										#Check translation of nonfixed bodies
+			
+			self.assertTrue(abs(O.bodies[id_fixed_rot].state.pos[0]-10.0*sin(pi/angVelTemp*O.iter))<tolerance)			#Check rotation of fixed bodies X
+			self.assertTrue(abs(O.bodies[id_fixed_rot].state.pos[2]-10.0*cos(pi/angVelTemp*O.iter))<tolerance)			#Check rotation of fixed bodies Y
+			self.assertTrue(abs(O.bodies[id_fixed_rot].state.ori.toAxisAngle()[1]-Quaternion(Vector3(0.0,1.0,0.0),pi/angVelTemp*O.iter).toAxisAngle()[1])<tolerance)		#Check rotation of fixed bodies, angle
+			
+			self.assertTrue(abs(O.bodies[id_nonfixed_rot].state.pos[0] - 10*sin(pi/angVelTemp*O.iter))<tolerance)		#Check rotation of nonfixed bodies X
+			self.assertTrue(abs(O.bodies[id_nonfixed_rot].state.pos[2] - 10*cos(pi/angVelTemp*O.iter))<tolerance)		#Check rotation of nonfixed bodies Y
+			self.assertTrue(abs(O.bodies[id_nonfixed_rot].state.ori.toAxisAngle()[1]-Quaternion(Vector3(0.0,1.0,0.0),pi/angVelTemp*O.iter).toAxisAngle()[1])<tolerance)		#Check rotation of nonfixed bodies, angle
+						
+			self.assertTrue(abs(O.bodies[id_fixed_helix].state.pos[0] - 10*sin(pi/angVelTemp*O.iter))<tolerance)		#Check helixEngine of fixed bodies X
+			self.assertTrue(abs(O.bodies[id_fixed_helix].state.pos[2] - 10*cos(pi/angVelTemp*O.iter))<tolerance)		#Check helixEngine of fixed bodies Y
+			self.assertTrue(abs(O.bodies[id_fixed_helix].state.pos[1]-20.0 - O.iter)<tolerance)		#Check helixEngine of fixed bodies Z
+			
+			self.assertTrue(abs(O.bodies[id_nonfixed_helix].state.pos[0] - 10*sin(pi/angVelTemp*O.iter))<tolerance)		#Check helixEngine of nonfixed bodies X
+			self.assertTrue(abs(O.bodies[id_nonfixed_helix].state.pos[2] - 10*cos(pi/angVelTemp*O.iter))<tolerance)		#Check helixEngine of nonfixed bodies Y
+			self.assertTrue(abs(O.bodies[id_nonfixed_helix].state.pos[1]-25.0 - O.iter)<tolerance)		#Check helixEngine of nonfixed bodies Z
+
+

=== modified file 'py/tests/pbc.py'
--- py/tests/pbc.py	2011-01-19 18:22:56 +0000
+++ py/tests/pbc.py	2011-01-20 14:55:15 +0000
@@ -18,7 +18,7 @@
 	# prefix test names with PBC: 
 	def setUp(self):
 		O.reset(); O.periodic=True;
-		O.cell.setRefSize(Vector3(2.5,2.5,3))
+		O.cell.refSize=(2.5,2.5,3)
 		self.cellDist=Vector3i(0,0,10) # how many cells away we go
 		self.relDist=Vector3(0,.999999999999999999,0) # rel position of the 2nd ball within the cell
 		self.initVel=Vector3(0,0,5)
@@ -31,6 +31,10 @@
 		O.cell.velGrad=Matrix3(0,0,0, 0,0,0, 0,0,-1)
 		O.cell.homoDeform=3
 		O.dt=0 # do not change positions with dt=0 in NewtonIntegrator, but still update velocities from velGrad
+	def testRefSize(self):
+		"PBC: Hsize reflects changes of refSize"
+		O.cell.refSize=(2.55,11,45)
+		self.assert_(O.cell.Hsize==Matrix3(2.55,0,0, 0,11,0, 0,0,45));
 	def testHomotheticResizeVel(self):
 		"PBC: homothetic cell deformation adjusts particle velocity (homoDeform==3)"
 		O.dt=1e-5

=== modified file 'py/tests/wrapper.py'
--- py/tests/wrapper.py	2010-10-19 14:57:27 +0000
+++ py/tests/wrapper.py	2011-01-20 14:55:15 +0000
@@ -14,8 +14,6 @@
 from yade import system
 from yade import *
 
-
-
 allClasses=system.childClasses('Serializable')
 
 class TestObjectInstantiation(unittest.TestCase):
@@ -65,6 +63,36 @@
 		# accessing invalid attributes raises AttributeError
 		self.assertRaises(AttributeError,lambda: Sphere(attributeThatDoesntExist=42))
 		self.assertRaises(AttributeError,lambda: Sphere().attributeThatDoesntExist)
+	##
+	## attribute flags
+	##
+	def testTriggerPostLoad(self):
+		'Core: Attr::triggerPostLoad'
+		# TranslationEngine normalizes translationAxis automatically
+		# anything else could be tested
+		te=TranslationEngine();
+		te.translationAxis=(0,2,0)
+		self.assert_(te.translationAxis==(0,1,0))
+	def testHidden(self):
+		'Core: Attr::hidden'
+		# hidden attributes are not wrapped in python at all
+		self.assert_(not hasattr(Interaction(),'iterLastSeen'))
+	def testNoSave(self):
+		'Core: Attr::noSave'
+		# update bound of the particle
+		O.bodies.append(utils.sphere((0,0,0),1))
+		O.engines=[InsertionSortCollider([Bo1_Sphere_Aabb()]),NewtonIntegrator()]
+		O.step()
+		O.saveTmp()
+		mn0=Vector3(O.bodies[0].bound.min)
+		O.reload()
+		mn1=Vector3(O.bodies[0].bound.min)
+		# check that the minimum is not saved
+		self.assert_(not isnan(mn0[0]))
+		self.assert_(isnan(mn1[0]))
+	def _testReadonly(self):
+		'Core: Attr::readonly'
+		self.assertRaises(AttributeError,lambda: setattr(Body(),'id',3))
 	
 class TestEigenWrapper(unittest.TestCase):
 	def assertSeqAlmostEqual(self,v1,v2):

=== modified file 'scripts/test/facet-sphere-ViscElBasic-peri.py'
--- scripts/test/facet-sphere-ViscElBasic-peri.py	2011-01-19 18:22:56 +0000
+++ scripts/test/facet-sphere-ViscElBasic-peri.py	2011-01-20 14:55:15 +0000
@@ -45,7 +45,7 @@
 ]
 
 O.periodic=True
-O.cell.setRefSize(Vector3(1,1,1))
+O.cell.refSize=(1,1,1)
 
 O.dt=.01*tc
 

=== modified file 'scripts/test/peri3dController_example1.py'
--- scripts/test/peri3dController_example1.py	2010-10-17 01:06:13 +0000
+++ scripts/test/peri3dController_example1.py	2011-01-20 14:55:15 +0000
@@ -61,5 +61,5 @@
 O.step()
 bo1s.aabbEnlargeFactor=ig2ss.distFactor=-1
 
-O.run(); O.wait()
+O.run(); #O.wait()
 plot.plot()

=== modified file 'scripts/test/peri3dController_shear.py'
--- scripts/test/peri3dController_shear.py	2011-01-19 18:22:56 +0000
+++ scripts/test/peri3dController_shear.py	2011-01-20 14:55:15 +0000
@@ -55,6 +55,7 @@
 
 renderer=qt.Renderer()
 renderer.intrPhys,renderer.shape=True,False
+Gl1_CpmPhys.dmgLabel=False
 qt.View()
 O.run()
 #plot.plot()

=== modified file 'scripts/test/peri8.py'
--- scripts/test/peri8.py	2011-01-19 18:22:56 +0000
+++ scripts/test/peri8.py	2011-01-20 14:55:15 +0000
@@ -3,7 +3,7 @@
 	[utils.sphere(c,r) for c in [(r,r,r),(3*r,r,r),(3*r,3*r,r),(r,3*r,r),(r,r,3*r),(3*r,r,3*r),(3*r,3*r,3*r),(r,3*r,3*r)]]
 )
 O.periodic=True
-O.cell.setRefSize((a,a,a))
+O.cell.refSize=(a,a,a)
 zRot=-pi/4.
-O.cell.setTrsf(Matrix3(cos(zRot),-sin(zRot),0,sin(zRot),cos(zRot),0,0,0,1))
+O.cell.trsf=Matrix3(cos(zRot),-sin(zRot),0,sin(zRot),cos(zRot),0,0,0,1)
 p7=O.bodies[7].state.pos

=== modified file 'scripts/test/periodic-compress.py'
--- scripts/test/periodic-compress.py	2011-01-19 18:22:56 +0000
+++ scripts/test/periodic-compress.py	2011-01-20 14:55:15 +0000
@@ -1,5 +1,5 @@
 O.periodic=True
-O.cell.setRefSize(Vector3(20,20,10))
+O.cell.refSize=(20,20,10)
 from yade import pack,log,timing
 O.materials.append(FrictMat(young=30e9,density=2400))
 p=pack.SpherePack()

=== modified file 'scripts/test/periodic-geom-compare.py'
--- scripts/test/periodic-geom-compare.py	2011-01-19 18:22:56 +0000
+++ scripts/test/periodic-geom-compare.py	2011-01-20 14:55:15 +0000
@@ -6,8 +6,8 @@
 #log.setLevel('PeriTriaxController',log.DEBUG)
 #log.setLevel('Shop',log.TRACE)
 O.periodic=True
-O.cell.setRefSize(Vector3(.1,.1,.1))
-O.cell.setTrsf(Matrix3().Identity);
+O.cell.refSize=(.1,.1,.1)
+O.cell.trsf=Matrix3().Identity;
 
 sp=pack.SpherePack()
 radius=5e-3

=== modified file 'scripts/test/periodic-grow.py'
--- scripts/test/periodic-grow.py	2011-01-19 18:22:56 +0000
+++ scripts/test/periodic-grow.py	2011-01-20 14:55:15 +0000
@@ -19,7 +19,7 @@
 cubeSize=20
 # absolute positioning of the cell is not important
 O.periodic=True
-O.cell.setRefSize(Vector3(cubeSize,cubeSize,cubeSize))
+O.cell.refSize=(cubeSize,cubeSize,cubeSize)
 O.dt=utils.PWaveTimeStep()
 O.saveTmp()
 from yade import qt

=== modified file 'scripts/test/periodic-shear.py'
--- scripts/test/periodic-shear.py	2011-01-19 18:22:56 +0000
+++ scripts/test/periodic-shear.py	2011-01-20 14:55:15 +0000
@@ -1,5 +1,5 @@
 O.periodic=True
-O.cell.setRefSize(Vector3(.55,.55,.55))
+O.cell.refSize=(.55,.55,.55)
 O.bodies.append(utils.facet([[.4,.0001,.3],[.2,.0001,.3],[.3,.2,.2]]))
 O.bodies.append(utils.sphere([.3,.1,.4],.05,dynamic=True))
 O.bodies.append(utils.sphere([.200001,.2000001,.4],.05,dynamic=False))
@@ -26,7 +26,7 @@
 #	O.cellShear=Vector3(.2*sin(g),.2*cos(pi*g),.2*sin(2*g)+.2*cos(3*g))
 #	time.sleep(0.001)
 #	g+=1e-3
-O.cell.setTrsf(Matrix3(1,0,0, 0,1,.5, 0,0,1))
+O.cell.trsf=Matrix3(1,0,0, 0,1,.5, 0,0,1)
 O.dt=2e-2*utils.PWaveTimeStep()
 O.step()
 O.saveTmp()

=== modified file 'scripts/test/periodic-simple-shear.py'
--- scripts/test/periodic-simple-shear.py	2011-01-19 18:22:56 +0000
+++ scripts/test/periodic-simple-shear.py	2011-01-20 14:55:15 +0000
@@ -5,7 +5,7 @@
 from yade import pack,log,qt
 log.setLevel('PeriTriaxController',log.TRACE)
 O.periodic=True
-O.cell.setRefSize(Vector3(.1,.1,.1))
+O.cell.refSize=(.1,.1,.1)
 #O.cell.Hsize=Matrix3(0.1,0,0, 0,0.1,0, 0,0,0.1)
 sp=pack.SpherePack()
 radius=5e-3

=== modified file 'scripts/test/periodic-simple.py'
--- scripts/test/periodic-simple.py	2011-01-19 18:22:56 +0000
+++ scripts/test/periodic-simple.py	2011-01-20 14:55:15 +0000
@@ -24,7 +24,7 @@
 O.bodies.appendClumped([utils.sphere([0,4,8],.8),utils.sphere([0,5,7],.6)])
 # sets up the periodic cell
 O.periodic=True
-O.cell.setRefSize(Vector3(10,10,10))
+O.cell.refSize=(10,10,10)
 # normally handled in by the simulation... but we want to have the rendering right before start
 O.cell.postProcessAttributes()
 O.dt=.1*utils.PWaveTimeStep()

=== modified file 'scripts/test/periodic-triax.py'
--- scripts/test/periodic-triax.py	2011-01-19 18:22:56 +0000
+++ scripts/test/periodic-triax.py	2011-01-20 14:55:15 +0000
@@ -5,7 +5,7 @@
 from yade import pack,log,qt
 log.setLevel('PeriTriaxController',log.TRACE)
 O.periodic=True
-O.cell.setRefSize(Vector3(.1,.1,.1))
+O.cell.refSize=(.1,.1,.1)
 #O.cell.Hsize=Matrix3(0.1,0,0, 0,0.1,0, 0,0,0.1)
 sp=pack.SpherePack()
 radius=5e-3

=== modified file 'scripts/test/sphere-sphere-ViscElBasic-peri.py'
--- scripts/test/sphere-sphere-ViscElBasic-peri.py	2011-01-19 18:22:56 +0000
+++ scripts/test/sphere-sphere-ViscElBasic-peri.py	2011-01-20 14:55:15 +0000
@@ -36,7 +36,7 @@
 ]
 
 O.periodic=True
-O.cell.setRefSize(Vector3(1,1,1))
+O.cell.refSize=(1,1,1)
 
 O.dt=.01*tc
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