Merge commit '0836c2fc'

Merge examples

examples/Pre/wall2D/test_exploded_deformable_bricks/command.py

@@ -174,7 +174,7 @@ for k in xrange(1, nb_steps + 1, 1):
    utilities_logMes('COMPUTE DOF, FIELDS, etc.')
    mecaMAILx_ComputeDof()
    RBDY2_ComputeDof()
-   mecaMAILx_ComputeBulk()
+   mecaMAILx_ComputeField()
    #
    utilities_logMes('UPDATE DOF, FIELDS')
    TimeEvolution_UpdateStep()

examples/RIGID_2D/1024DK_BoxJC_ElectricalConduction/command.py

-import os,sys
-
-sys.path.append('/Users/mrenouf/GitLab_LMGC90/build_dev_rc2015')
-
 from pylmgc90.chipy import *
 
 checkDirectories()

examples/RIGID_2D/1024DK_BoxJC_ThermalConduction/command.py

-import os,sys
-
-sys.path.append('/Users/mrenouf/GitLab_LMGC90/build_dev_rc2015')
-
 from pylmgc90.chipy import *
 
 checkDirectories()

examples/RIGID_2D/1024DK_BoxJC_ThermalConduction/command_for_dummies.py

-import os,sys
-
-sys.path.append('/Users/mrenouf/GitLab_LMGC90/build_dev_rc2015')
 
 from pylmgc90.chipy import *
 
@@ -99,6 +96,7 @@ for i in xrange(0,nb_steps_ther,1):
    IncrementStep()
    mp_solver_RecupTemperature()
    mp_solver_SolveThermoProblem()
+   mecaMAILx_ComputeField()
    UpdateStep()
 
    ### postpro ###

examples/RIGID_3D/thermal3D/command.py

 import os,sys
 
-sys.path.append('/Users/mrenouf/GitLab_LMGC90/build_dev_rc2015')
-
 from pylmgc90.chipy import *
 from numpy import *
 
@@ -99,7 +97,7 @@ nbspher = SPHER_GetNbSPHER()
 
 Ts =  np.zeros([nbspher])
 
-spher2rbdy3 = SPHER_GetPtrSPHER2RBDY3()
+spher2rbdy3 = SPHER_GetPtrSPHER2BDYTY()
 
 #
 for i in xrange(0,nb_iter,1):

examples/Tutorials/pre/DK_BoxJC/1024DK_BoxJC.ipynb

+%% Cell type:markdown id: tags:
+
+# Biaxial compression of a rectangular box filled with disks
+
+F. Dubois - 2016
+
+%% Cell type:markdown id: tags:
+
+## Pre-processing
+
+%% Cell type:markdown id: tags:
+
+Initialisation
+
+%% Cell type:code id: tags:
+
+``` python
+import numpy as np
+from pylmgc90.pre_lmgc import *
+if not os.path.isdir('./DATBOX'):
+  os.mkdir('./DATBOX')
+
+# 2D
+dim = 2
+
+# containers
+#   * bodies
+bodies = avatars()
+#   * materials
+mat = materials()
+#   * see tables
+svs = see_tables()
+#   * contact laws
+tacts = tact_behavs()
+
+# creations de deux materiaux
+tdur = material(name='TDURx',type='RIGID',density=1000.)
+plex = material(name='PLEXx',type='RIGID',density=100.)
+mat.addMaterial(tdur,plex)
+
+# on cree un modele de rigide
+mod = model(name='rigid', type='MECAx', element='Rxx2D', dimension=dim)
+
+# on genere 1000 particules
+nb_particles=1000
+
+# distribtion aleatoire dans [0.5, 2.[
+radii=granulo_Random(nb_particles, 0.5, 2.)
+
+# on recupere le plus petit et le plus grand rayon
+radius_min=min(radii)
+radius_max=max(radii)
+
+# depot dans une boite rectangulaire
+lx = 75.
+ly = 50.
+[nb_remaining_particles, coor]=depositInBox2D(radii, lx, ly)
+
+# si toutes les particules deposees n'ont pas ete conservees
+if (nb_remaining_particles < nb_particles):
+   # on affiche un avertissement
+   print "Warning: granulometry changed, since some particles were removed!"
+
+# boucle d'ajout des disques :
+for i in xrange(0,nb_remaining_particles,1):
+   # creation un nouveau disque rigide, constitue du materiau plex
+   body=rigidDisk(r=radii[i], center=coor[2*i : 2*(i + 1)],
+      model=mod, material=plex, color='BLEUx')
+   # ajout du disque dans le conteneur de corps
+   bodies += body
+
+# ajout d'une boite lisse, i.e. faite de joncs :
+
+# on declare un corps par paroi
+down = rigidJonc(axe1=0.5*lx+radius_max, axe2=radius_max, center=[0.5*lx, -radius_max],
+                 model=mod, material=tdur, color='WALLx')
+up   = rigidJonc(axe1=0.5*lx+radius_max, axe2=radius_max, center=[0.5*lx, ly+radius_max],
+                 model=mod, material=tdur, color='WALLx')
+left = rigidJonc(axe1=0.5*ly+radius_max, axe2=radius_max, center=[-radius_max, 0.5*ly],
+                 model=mod, material=tdur, color='WALLx')
+right= rigidJonc(axe1=0.5*ly+radius_max, axe2=radius_max, center=[lx+radius_max, 0.5*ly],
+                 model=mod, material=tdur, color='WALLx')
+
+# on ajoute les parois a la liste des corps
+bodies += down; bodies += up; bodies += left; bodies += right
+
+# on tourne les parois verticales (par rapport a leur propres
+# centre d'inertie)
+left.rotate(psi=-math.pi/2., center=left.nodes[1].coor)
+right.rotate(psi=math.pi/2., center=right.nodes[1].coor)
+
+# on fixe les parois
+down.imposeDrivenDof(component=[1, 2, 3], dofty='vlocy')
+up.imposeDrivenDof(component=[1, 2, 3], dofty='vlocy')
+left.imposeDrivenDof(component=[1, 2, 3], dofty='vlocy')
+right.imposeDrivenDof(component=[1, 2, 3], dofty='vlocy')
+
+# gestion des interactions :
+#   * declaration des lois
+#       - entre particules
+ldkdk=tact_behav(name='iqsc0',type='IQS_CLB',fric=0.3)
+tacts+=ldkdk
+#       - avec les parois
+ldkjc=tact_behav(name='iqsc1',type='IQS_CLB',fric=0.5)
+tacts+=ldkjc
+#   * declaration des tables de visibilite
+#       - entre particules
+svdkdk = see_table(CorpsCandidat='RBDY2',candidat='DISKx',
+   colorCandidat='BLEUx',behav=ldkdk, CorpsAntagoniste='RBDY2',
+   antagoniste='DISKx',colorAntagoniste='BLEUx',alert=0.1*radius_min)
+svs+=svdkdk
+#       - avec les parois
+svdkjc = see_table(CorpsCandidat='RBDY2',candidat='DISKx',
+   colorCandidat='BLEUx',behav=ldkjc, CorpsAntagoniste='RBDY2',
+   antagoniste='JONCx',colorAntagoniste='WALLx',alert=0.1*radius_min)
+svs+=svdkjc
+
+# ecriture des fichiers
+writeBodies(bodies,chemin='DATBOX/')
+writeBulkBehav(mat,chemin='DATBOX/')
+writeTactBehav(tacts,svs,chemin='DATBOX/')
+writeDrvDof(bodies,chemin='DATBOX/')
+writeDofIni(bodies,chemin='DATBOX/')
+writeVlocRlocIni(chemin='DATBOX/')
+
+try:
+  visuAvatars(bodies)
+except:
+  pass
+```
+
+%% Cell type:code id: tags:
+
+``` python
+```

examples/Tutorials/pre/avatar/RigidAvatar.ipynb

+%% Cell type:markdown id: tags:
+
+# How to build a rigid avatar
+
+F. Dubois 2016
+
+%% Cell type:markdown id: tags:
+
+All avatars are made of nodes, elements, contactors and need a material and a model.
+
+%% Cell type:markdown id: tags:
+
+## 2D Case
+
+%% Cell type:code id: tags:
+
+``` python
+#Initialization
+from pylmgc90.pre_lmgc import *
+# 2D
+dim = 2
+```
+
+%%%% Output: stream
+
+    Info : med file reading module not available
+
+%% Cell type:markdown id: tags:
+
+Defining a material suitable for rigid objects.
+
+%% Cell type:code id: tags:
+
+``` python
+mut = material(name='TDURx',type='RIGID',density=1000.)
+```
+
+%% Cell type:markdown id: tags:
+
+Defining a model suitable for rigid objects.
+
+%% Cell type:code id: tags:
+
+``` python
+mod = model(name='rigid', type='MECAx', element='Rxx2D', dimension=dim)
+```
+
+%% Cell type:markdown id: tags:
+
+Defining an empty avatar
+
+%% Cell type:code id: tags:
+
+``` python
+disk = avatar(type='RBDY2',dimension=2)
+
+## some introspection
+## what is disk ?
+#help(disk)
+## what is nodes in disk ?
+#help(disk.nodes)
+## what are the keys in nodes ?
+#print disk.nodes.viewkeys()
+## what are the values in nodes ?
+#print disk.nodes.viewvalues()
+```
+
+%% Cell type:markdown id: tags:
+
+Creating a node and adding it to the avatar (number MUST be 1)
+
+%% Cell type:code id: tags:
+
+``` python
+no = node(type='NO2xx',coor=numpy.array([0.,0.1]),number=1)
+
+## some introspection
+## what is no ?
+#help(no)
+## what is containing no ?
+#dir(no)
+#print no.coor
+
+# adding no to avatar
+disk.addNode( no )
+
+## some introspection
+## does no.nodes change ?
+#print disk.nodes.viewkeys()
+#print disk.nodes.viewvalues()
+## key to access to value of first node stored
+#id=disk.nodes.keys()[0]
+#print 'id= ',id
+## what is this value ?
+#help(disk.nodes[id])
+#dir(disk.nodes[id])
+#print disk.nodes[id].coor
+#print disk.nodes[id].getCoor()
+#print disk.nodes[id].number
+#print disk.nodes.values()[0].coor
+```
+
+%% Cell type:markdown id: tags:
+
+Creating an element and adding it to the avatar
+
+%% Cell type:code id: tags:
+
+``` python
+disk.addBulk( rigid2d() )
+
+## some introspection
+#help(disk.bulks)
+#print disk.bulks.keys()
+#id=disk.bulks.keys()[0]
+#help(disk.bulks[id])
+#dir(disk.bulks[id])
+#print disk.bulks[id].connectivity
+```
+
+%% Cell type:markdown id: tags:
+
+ We need groups to add model/material, contactors, drivendof, etc.
+
+%% Cell type:code id: tags:
+
+``` python
+## does my object contain groups ?
+#dir(disk.groups)
+#print disk.groups.viewkeys()
+
+#
+disk.defineGroups()
+
+## does my object contain groups ?
+#print disk.groups.viewkeys()
+## what is group 'all'?
+#help(disk.groups['all'])
+#dir(disk.groups['all'])
+#help(disk.groups['all'].bulks)
+#dir(disk.groups['all'])
+#print disk.groups['all'].bulks.keys()
+#print disk.groups['all'].bulks[0]
+#print disk.groups['all'].nodes.keys()
+#print disk.groups['all'].contactors.keys()
+```
+
+%% Cell type:markdown id: tags:
+
+Adding model and material (default added to 'all').
+
+%% Cell type:code id: tags:
+
+``` python
+disk.defineModel(model=mod)
+disk.defineMaterial(material=mut)
+```
+
+%% Cell type:markdown id: tags:
+
+Adding contactor (default added to 'all')
+
+%% Cell type:code id: tags:
+
+``` python
+disk.addContactors(type='DISKx', color='BLUEx', byrd=1.)
+```
+
+%% Cell type:markdown id: tags:
+
+Needs to compute some internal values (mass, inertia, frame, etc)
+
+%% Cell type:code id: tags:
+
+``` python
+disk.computeRigidProperties()
+```
+
+%% Cell type:markdown id: tags:
+
+Some magic function
+
+%% Cell type:code id: tags:
+
+``` python
+disk2=rigidDisk(r=1., center=[2., 2.], model=mod, material=mut, color='BLUEx')
+```
+
+%% Cell type:code id: tags:
+
+``` python
+#Draw
+bodies = avatars()
+bodies.addAvatar(disk)
+bodies.addAvatar(disk2)
+visuAvatars(bodies)
+```

examples/Tutorials/pre/deposit/Deposit2D.ipynb

+%% Cell type:markdown id: tags:
+
+# Managing 2D deposit
+
+F. Dubois - 2016
+
+%% Cell type:markdown id: tags:
+
+Importing necessary modules for the tutorial
+
+%% Cell type:code id: tags:
+
+``` python
+%matplotlib inline
+
+import os,sys
+import numpy
+import matplotlib.pyplot as plt
+
+from pylmgc90.pre_lmgc import *
+```
+
+%% Cell type:markdown id: tags:
+
+For this tutorial we need a function able to draw circles.
+
+%% Cell type:code id: tags:
+
+``` python
+def draw(coor,radii):
+
+  plt.axes()
+
+  for k in range(len(radii)):
+    circle = plt.Circle((coor[k,0], coor[k,1]), radius=radii[k], fc='y')
+    plt.gca().add_patch(circle)
+
+  plt.axis('scaled')
+  plt.show()
+```
+
+%% Cell type:markdown id: tags:
+
+Nice we can draw ... Mickey Mouse !
+
+%% Cell type:code id: tags:
+
+``` python
+coor=numpy.array([[0., 0.],[1.,1.],[-1.,1.],[0.,0.],[0.5,0.5],[-0.5,0.5]])
+rayon=[1.,0.5,0.5,0.2,0.1,0.3]
+draw(coor,rayon)
+```
+
+%% Cell type:markdown id: tags:
+
+Lets consider a more interesting problem. We need a set of radius.
+
+%% Cell type:code id: tags:
+
+``` python
+# Generating a list of radius
+nb_particles = 10000
+radius_min   = 1.0
+radius_max   = 2.5
+radii = granulo_Random(nb_particles, radius_min, radius_max)
+```
+
+%% Cell type:markdown id: tags:
+
+Now we have to compute the positions of these disks.
+
+%% Cell type:code id: tags:
+
+``` python
+case=0
+
+if case == 0:
+  # putting particles in a box [0.,0.]*[150.,100.]
+  lx = 150.
+  ly = 100.
+  [nb_laid_particles, coors] = depositInBox2D(radii,lx,ly)
+
+elif case == 1:
+  rext=150.
+  [nb_laid_particles, coors]=depositInDisk2D(radii, rext)
+
+elif case == 2:
+    rext=150.
+    rint=100.
+    [nb_laid_particles, coors]=depositInCouetteD(radii, rint, rext)
+
+elif case == 3:
+    rext=150.
+    [nb_laid_particles, coors]=depositInDrum2D(radii,rext)
+
+elif case == 4:
+  # putting particles on a square lattice
+  coors=squareLattice2D(10, 10, 2*radius_max, x0=0., y0=0.)
+  #print numpy.shape(coors)
+  nb_laid_particles=numpy.shape(coors)[0]/2
+
+elif case == 5:
+  coors=triangularLattice2D(20, 20, 2*radius_max, x0=0., y0=0.)
+  nb_laid_particles=numpy.shape(coors)[0]/2
+
+
+
+# reducing coors & radii arrays to useful part
+coors = coors[0:2*nb_laid_particles]
+radii = radii[0:nb_laid_particles]
+```
+
+%% Cell type:markdown id: tags:
+
+Lets draw
+
+%% Cell type:code id: tags:
+
+``` python
+print 'Real number of particles: ',numpy.shape(radii)
+
+# drawing
+coors=numpy.reshape(coors,(nb_laid_particles,2))
+draw(coors,radii)
+```

examples/Tutorials/pre/granulo/granulometry.ipynb

+%% Cell type:markdown id: tags:
+
+# Managing granulometry
+
+F. Dubois - 2016
+
+%% Cell type:markdown id: tags:
+
+Importing necessary modules
+
+%% Cell type:code id: tags:
+
+``` python
+%matplotlib inline
+%config InlineBackend.figure_formats = {'svg',}
+#%config InlineBackend.figure_formats = {'png', 'retina'}
+
+import os,sys
+import numpy
+import math
+import scipy
+import scipy.special
+import random
+import matplotlib.pyplot as plt
+
+# Seaborn, useful for graphics
+import seaborn as sns
+
+# JB's favorite Seaborn settings for notebooks
+rc = {'lines.linewidth': 2,
+      'axes.labelsize': 18,
+      'axes.titlesize': 18,
+      'axes.facecolor': 'DFDFE5'}
+sns.set_context('notebook', rc=rc)
+sns.set_style('darkgrid', rc=rc)
+
+
+# Import Bokeh modules for interactive plotting
+import bokeh.io
+import bokeh.mpl
+import bokeh.plotting
+bokeh.io.output_notebook()
+
+from pylmgc90.pre_lmgc import *
+```
+
+%% Cell type:markdown id: tags:
+
+A function to draw the cumulated volume of particles
+
+%% Cell type:code id: tags:
+
+``` python
+def draw_granulo(radii):
+  """
+     A function to draw the cumulative volume occupied by a list of particles with respect to the radius
+
+     :param radii: an array of radii
+  """
+
+  rd = numpy.sort(radii)
+
+  # computing total volume (4pi/3 voluntarily omitted)
+  vv=0.
+  for radius in radii:
+    vv+=math.pow(radius,3)
+
+  # ecriture granulo