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Message #08067
[Branch ~yade-dev/yade/trunk] Rev 2962: - make body iterators jump empty slots, as suggested and discussed here: http://www.mail-archive....
------------------------------------------------------------
revno: 2962
committer: Bruno Chareyre <bruno.chareyre@xxxxxxxxxxx>
branch nick: trunk
timestamp: Wed 2011-11-23 13:05:49 +0100
message:
- make body iterators jump empty slots, as suggested and discussed here: http://www.mail-archive.com/yade-dev@xxxxxxxxxxxxxxxxxxx/msg07406.html
- revert the (now useless) fix of r2961, similar tests can be removed in many places after the change in pointer logic is well tested.
- remove a script, as agreed by Christian (https://answers.launchpad.net/yade/+question/178830)
removed:
examples/generate-psd-with-poro-example.py
modified:
core/BodyContainer.hpp
pkg/dem/GlobalStiffnessTimeStepper.cpp
--
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=== modified file 'core/BodyContainer.hpp'
--- core/BodyContainer.hpp 2010-11-30 13:51:41 +0000
+++ core/BodyContainer.hpp 2011-11-23 12:05:49 +0000
@@ -59,9 +59,18 @@
#endif
public:
friend class InteractionContainer; // accesses the body vector directly
+
+ //An iterator that will automatically jump slots with null bodies
+ class smart_iterator : public ContainerT::iterator {
+ public:
+ ContainerT::iterator end;
+ smart_iterator& operator++() {do {ContainerT::iterator::operator++();} while (!(this->operator*()) && end!=(*this)); return *this;}
+ smart_iterator operator++(int) {smart_iterator temp(*this); operator++(); return temp;}
+ smart_iterator& operator=(const ContainerT::iterator& rhs) {ContainerT::iterator::operator=(rhs); return *this;}
+ };
- typedef ContainerT::iterator iterator;
- typedef ContainerT::const_iterator const_iterator;
+ typedef smart_iterator iterator;
+ typedef const smart_iterator const_iterator;
BodyContainer();
virtual ~BodyContainer();
@@ -70,10 +79,11 @@
// mimick some STL api
void clear();
- iterator begin() { return body.begin(); }
- iterator end() { return body.end(); }
- const_iterator begin() const { return body.begin(); }
- const_iterator end() const { return body.end(); }
+ iterator begin() { iterator temp; temp=(body.begin()); temp.end=(body.end()); return temp;}
+ iterator end() { iterator temp; temp= body.end(); return temp;}
+ const_iterator begin() const { return begin();}
+ const_iterator end() const { return end();}
+
size_t size() const { return body.size(); }
shared_ptr<Body>& operator[](unsigned int id){ return body[id];}
const shared_ptr<Body>& operator[](unsigned int id) const { return body[id]; }
=== removed file 'examples/generate-psd-with-poro-example.py'
--- examples/generate-psd-with-poro-example.py 2011-11-16 12:43:43 +0000
+++ examples/generate-psd-with-poro-example.py 1970-01-01 00:00:00 +0000
@@ -1,170 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-
-"""
-This example shows how to generate a particle packing with given particle-size distribution curve (psd) and a given porosity.
-This method works well for loose packings and low number of particles. Be careful, when particle sizes are low!
-
-First step is to generate the particles with decreased radii (see radius denominator, rad_denom). In the next step the radius
-of all particles is expanded step-by-step by radius multipliers (see rad_mul). After each expansion high overlaps can occur.
-Therefore the model has to calm down before the next expansion can be made (see calm() function).
-"""
-
-# USER INPUT :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-
-rho_p = 2650 #density of particles
-friction=0.5 #friction coefficient
-angle=atan(friction)
-
-initial_porosity = 0.4 #set a target porosity
-
-#SET GRAIN DISTRIBUTION:
-#diameter at the borders of the classes from lowest to highest in [m]:
-dia = [0.000063, 0.00009, 0.000125, 0.00018, 0.00025, 0.000355, 0.0005, 0.00071, 0.001, 0.002]
-num_borders = len(dia)
-
-#one-hundredth of volume-percent of classes out of sieve analysis:
-phi = [0.0004, 0.0046, 0.0234, 0.1467, 0.4657, 0.2886, 0.0641, 0.0071, 0.0011]
-num_classes = len(phi)
-
-#SET DIMENSIONS OF THE MODEL (only cuboid possible in actual version):
-x_cl = 0 #lower x coordinate in front
-y_cl = 0 #lower y coordinate in front
-z_cl = 0 #lower z coordinate in front
-x_cu = 0.002 #upper x coordinate in back
-y_cu = 0.002 #upper y coordinate in back
-z_cu = 0.002 #upper z coordinate in back
-
-#SET RADIUS MULTIPLIER CONSTANTS (for blowing up balls during generation process):
-rad_mul = [2, 1.8, 1.5, 1.2, 1.05]
-num_rad_mul = len(rad_mul)
-
-# END USER INPUT :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-
-
-# DEFINE MATERIALS AND ENGINES :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-
-id_FacetMat=O.materials.append(ViscElMat(kn=1e8,ks=1e8,cn=0.0,cs=0.0,frictionAngle=angle))
-id_SphereMat=O.materials.append(ViscElMat(kn=1e6,ks=1e6,cn=0.0,cs=0.0,density=rho_p,frictionAngle=angle))
-
-FacetMat=O.materials[id_FacetMat]
-SphereMat=O.materials[id_SphereMat]
-
-O.engines=[
- ForceResetter(),
- InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),
- InteractionLoop(
- [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()],
- [Ip2_ViscElMat_ViscElMat_ViscElPhys()],
- [Law2_ScGeom_ViscElPhys_Basic()],
- ),
- GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=1,timestepSafetyCoefficient=0.8, defaultDt=4*utils.PWaveTimeStep()),
- NewtonIntegrator(damping=0.7)
-]
-
-# END DEFINE MATERIALS AND ENGINES :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-
-
-# GENERATION PROCESS :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-
-V_c = (x_cu-x_cl)*(y_cu-y_cl)*(z_cu-z_cl) #total volume of cuboid
-V_part = V_c*(1-initial_porosity) #volume of all particles
-
-rad_denom = 1
-for ii in range(0,num_rad_mul):
- rad_denom = rad_denom*rad_mul[ii]
-
-#step1: calculation of volumes of spheres at borders
-rad_borders = [1]*num_borders
-Vg_borders = [1]*num_borders
-for ii in range(0,num_borders):
- rad_borders[ii] = 0.5*dia[ii] #get radii from diameters
- Vg_borders[ii] = 4*math.pi*(rad_borders[ii]*rad_borders[ii]*rad_borders[ii])/3 #volumes of spheres at borders
-
-#step2: calculation of numbers of spheres of spheres in every class
-Vd_classes = [1]*num_classes
-rad_d = [1]*num_classes
-V_classes = [1]*num_classes
-num_spheres = [1]*num_classes
-for ii in range(0,num_classes):
- Vd_classes[ii] = (Vg_borders[ii+1]+Vg_borders[ii])/2.0 #average volumes in every class
- rad_d[ii] = pow(3*Vd_classes[ii]/(4*math.pi),1.0/3.0) #average radii in every class
- V_classes[ii] = phi[ii]*V_part #particle volumes in every class
- #numbers of spheres in every class:
- num_spheres[ii] = int(round((3*V_classes[ii])/(4*math.pi*rad_d[ii]*rad_d[ii]*rad_d[ii])))
-
-sum_spheres = -1
-#step3: get random coordinates and radii and generate particles
-for jj in range(0,num_classes):
- for ii in range(0,num_spheres[jj]):
- r_tmp = rad_borders[jj] + (rad_borders[jj+1] - rad_borders[jj])*random.random() #random radii
- x_tmp = r_tmp + x_cl + ((x_cu-x_cl) - 2*r_tmp)*random.random() #random coordinates x, y, z
- y_tmp = r_tmp + y_cl + ((y_cu-y_cl) - 2*r_tmp)*random.random()
- z_tmp = r_tmp + z_cl + ((z_cu-z_cl) - 2*r_tmp)*random.random()
- r_tmp = r_tmp/rad_denom #decrease radii for generation process
- sum_spheres=O.bodies.append(utils.sphere([x_tmp,y_tmp,z_tmp], material=SphereMat, radius=r_tmp, wire=False, highlight=False))#, color=(50,50,0)))
-
-O.bodies.append(geom.facetBox(((x_cu-x_cl)/2.0,(y_cu-y_cl)/2.0,(z_cu-z_cl)/2.0),((x_cu-x_cl)/2.0,(y_cu-y_cl)/2.0,(z_cu-z_cl)/2.0),fixed=True,material=FacetMat))
-
-# END GENERATION PROCESS :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-
-#DEFINITIONS:
-
-def calm():
- for ii in range(0,sum_spheres+1):
- O.bodies[ii].state.vel = Vector3(0,0,0)
- O.bodies[ii].state.angVel = Vector3(0,0,0)
-
-# RELAXATION PROCESS :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-
-from yade import qt
-v=qt.View()
-raw_input('press ENTER to start RELAXATION')
-
-O.engines=O.engines+[PyRunner(iterPeriod=10,command='calm()',label='calmLabel1')]
-O.run(1000,True)
-
-for ii in range(0,sum_spheres+1):
- O.bodies[ii].shape.radius=O.bodies[ii].shape.radius*rad_mul[0]
-print ('radius of particles increased by factor %f, step 1 of 5' % rad_mul[0])
-O.run(3000,True)
-
-for ii in range(0,sum_spheres+1):
- O.bodies[ii].shape.radius=O.bodies[ii].shape.radius*rad_mul[1]
-print ('radius of particles increased by factor %f, step 2 of 5' % rad_mul[1])
-O.run(3000,True)
-calmLabel1.dead=True
-O.engines=O.engines+[PyRunner(iterPeriod=20,command='calm()',label='calmLabel2')]
-O.run(3000,True)
-
-for ii in range(0,sum_spheres+1):
- O.bodies[ii].shape.radius=O.bodies[ii].shape.radius*rad_mul[2]
-print ('radius of particles increased by factor %f, step 3 of 5' % rad_mul[2])
-calmLabel2.dead=True
-O.engines=O.engines+[PyRunner(iterPeriod=10,command='calm()',label='calmLabel3')]
-O.run(7000,True)
-calmLabel3.dead=True
-O.engines=O.engines+[PyRunner(iterPeriod=20,command='calm()',label='calmLabel4')]
-O.run(7000,True)
-
-for ii in range(0,sum_spheres+1):
- O.bodies[ii].shape.radius=O.bodies[ii].shape.radius*rad_mul[3]
-print ('radius of particles increased by factor %f, step 4 of 5' % rad_mul[3])
-calmLabel4.dead=True
-O.engines=O.engines+[PyRunner(iterPeriod=10,command='calm()',label='calmLabel5')]
-O.run(25000,True)
-calmLabel5.dead=True
-O.engines=O.engines+[PyRunner(iterPeriod=20,command='calm()',label='calmLabel6')]
-O.run(25000,True)
-
-for ii in range(0,sum_spheres+1):
- O.bodies[ii].shape.radius=O.bodies[ii].shape.radius*rad_mul[4]
-print ('radius of particles increased by factor %f, step 5 of 5' % rad_mul[4])
-calmLabel6.dead=True
-O.engines=O.engines+[PyRunner(iterPeriod=10,command='calm()',label='calmLabel7')]
-O.run(25000,True)
-calmLabel7.dead=True
-O.engines=O.engines+[PyRunner(iterPeriod=20,command='calm()',label='calmLabel8')]
-O.run(25000,True)
-
-# END RELAXATION PROCESS :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
=== modified file 'pkg/dem/GlobalStiffnessTimeStepper.cpp'
--- pkg/dem/GlobalStiffnessTimeStepper.cpp 2011-11-18 12:25:48 +0000
+++ pkg/dem/GlobalStiffnessTimeStepper.cpp 2011-11-23 12:05:49 +0000
@@ -73,7 +73,6 @@
BodyContainer::iterator biEnd = bodies->end();
for( ; bi!=biEnd ; ++bi )
{
- if (!*bi) continue;
shared_ptr<Body> b = *bi;
if (b->isDynamic()) findTimeStepFromBody(b, ncb);
}
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