"""
Import geometry from various formats ('import' is python keyword, hence the name 'ymport').
"""
from yade.wrapper import *
from yade import utils
from minieigen import *
[docs]def textExt(fileName,format='x_y_z_r',shift=Vector3.Zero,scale=1.0,**kw):
"""Load sphere coordinates from file in specific format, returns a list of corresponding bodies; that may be inserted to the simulation with O.bodies.append().
:param str filename: file name
:param str format: the name of output format. Supported `x_y_z_r`(default), `x_y_z_r_matId`
:param [float,float,float] shift: [X,Y,Z] parameter moves the specimen.
:param float scale: factor scales the given data.
:param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.sphere`
:returns: list of spheres.
Lines starting with # are skipped
"""
infile = open(fileName,"r")
lines = infile.readlines()
infile.close()
ret=[]
for line in lines:
data = line.split()
if (data[0] == "#format"):
format=data[1]
continue
elif (data[0][0] == "#"): continue
if (format=='x_y_z_r'):
pos = Vector3(float(data[0]),float(data[1]),float(data[2]))
ret.append(utils.sphere(shift+scale*pos,scale*float(data[3]),**kw))
elif (format=='x_y_z_r_matId'):
pos = Vector3(float(data[0]),float(data[1]),float(data[2]))
ret.append(utils.sphere(shift+scale*pos,scale*float(data[3]),material=int(data[4]),**kw))
elif (format=='id_x_y_z_r_matId'):
pos = Vector3(float(data[1]),float(data[2]),float(data[3]))
ret.append(utils.sphere(shift+scale*pos,scale*float(data[4]),material=int(data[5]),**kw))
else:
raise RuntimeError("Please, specify a correct format output!");
return ret
[docs]def textClumps(fileName,shift=Vector3.Zero,discretization=0,orientation=Quaternion((0,1,0),0.0),scale=1.0,**kw):
"""Load clumps-members from file, insert them to the simulation.
:param str filename: file name
:param str format: the name of output format. Supported `x_y_z_r`(default), `x_y_z_r_clumpId`
:param [float,float,float] shift: [X,Y,Z] parameter moves the specimen.
:param float scale: factor scales the given data.
:param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.sphere`
:returns: list of spheres.
Lines starting with # are skipped
"""
infile = open(fileName,"r")
lines = infile.readlines()
infile.close()
ret=[]
curClump=[]
newClumpId = -1
for line in lines:
data = line.split()
if (data[0][0] == "#"): continue
pos = orientation*Vector3(float(data[0]),float(data[1]),float(data[2]))
if (newClumpId<0 or newClumpId==int(data[4])):
idD = curClump.append(utils.sphere(shift+scale*pos,scale*float(data[3]),**kw))
newClumpId = int(data[4])
else:
newClumpId = int(data[4])
ret.append(O.bodies.appendClumped(curClump,discretization=discretization))
curClump=[]
idD = curClump.append(utils.sphere(shift+scale*pos,scale*float(data[3]),**kw))
if (len(curClump)<>0):
ret.append(O.bodies.appendClumped(curClump,discretization=discretization))
# Set the mask to a clump the same as the first member of it
for i in range(len(ret)):
O.bodies[ret[i][0]].mask = O.bodies[ret[i][1][0]].mask
return ret
[docs]def text(fileName,shift=Vector3.Zero,scale=1.0,**kw):
"""Load sphere coordinates from file, returns a list of corresponding bodies; that may be inserted to the simulation with O.bodies.append().
:param string filename: file which has 4 colums [x, y, z, radius].
:param [float,float,float] shift: [X,Y,Z] parameter moves the specimen.
:param float scale: factor scales the given data.
:param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.sphere`
:returns: list of spheres.
Lines starting with # are skipped
"""
return textExt(fileName=fileName,format='x_y_z_r',shift=shift,scale=scale,**kw)
[docs]def stl(file, dynamic=None,fixed=True,wire=True,color=None,highlight=False,noBound=False,material=-1):
""" Import geometry from stl file, return list of created facets."""
imp = STLImporter()
facets=imp.ymport(file)
for b in facets:
b.shape.color=color if color else utils.randomColor()
b.shape.wire=wire
b.shape.highlight=highlight
pos=b.state.pos
utils._commonBodySetup(b,0,Vector3(0,0,0),material=material,pos=pos,noBound=noBound,dynamic=dynamic,fixed=fixed)
b.aspherical=False
return facets
[docs]def gts(meshfile,shift=(0,0,0),scale=1.0,**kw):
""" Read given meshfile in gts format.
:Parameters:
`meshfile`: string
name of the input file.
`shift`: [float,float,float]
[X,Y,Z] parameter moves the specimen.
`scale`: float
factor scales the given data.
`**kw`: (unused keyword arguments)
is passed to :yref:`yade.utils.facet`
:Returns: list of facets.
"""
import gts,yade.pack
surf=gts.read(open(meshfile))
surf.scale(scale)
surf.translate(shift)
yade.pack.gtsSurface2Facets(surf,**kw)
[docs]def gmsh(meshfile="file.mesh",shift=Vector3.Zero,scale=1.0,orientation=Quaternion((0,1,0),0.0),**kw):
""" Imports geometry from mesh file and creates facets.
: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 facets forming the specimen.
mesh files can be easily created with `GMSH <http://www.geuz.org/gmsh/>`_.
Example added to :ysrc:`examples/regular-sphere-pack/regular-sphere-pack.py`
Additional examples of mesh-files can be downloaded from
http://www-roc.inria.fr/gamma/download/download.php
"""
infile = open(meshfile,"r")
lines = infile.readlines()
infile.close()
nodelistVector3=[]
findVerticesString=0
while (lines[findVerticesString].split()[0]<>'Vertices'): #Find the string with the number of Vertices
findVerticesString+=1
findVerticesString+=1
numNodes = int(lines[findVerticesString].split()[0])
for i in range(numNodes):
nodelistVector3.append(Vector3(0.0,0.0,0.0))
id = 0
for line in lines[findVerticesString+1:numNodes+findVerticesString+1]:
data = line.split()
nodelistVector3[id] = orientation*Vector3(float(data[0])*scale,float(data[1])*scale,float(data[2])*scale)+shift
id += 1
findTriangleString=findVerticesString+numNodes
while (lines[findTriangleString].split()[0]<>'Triangles'): #Find the string with the number of Triangles
findTriangleString+=1
findTriangleString+=1
numTriangles = int(lines[findTriangleString].split()[0])
triList = []
for i in range(numTriangles):
triList.append([0,0,0,0])
tid = 0
for line in lines[findTriangleString+1:findTriangleString+numTriangles+1]:
data = line.split()
id1 = int(data[0])-1
id2 = int(data[1])-1
id3 = int(data[2])-1
triList[tid][0] = tid
triList[tid][1] = id1
triList[tid][2] = id2
triList[tid][3] = id3
tid += 1
ret=[]
for i in triList:
a=nodelistVector3[i[1]]
b=nodelistVector3[i[2]]
c=nodelistVector3[i[3]]
ret.append(utils.facet((nodelistVector3[i[1]],nodelistVector3[i[2]],nodelistVector3[i[3]]),**kw))
return ret
[docs]def gengeoFile(fileName="file.geo",shift=Vector3.Zero,scale=1.0,orientation=Quaternion((0,1,0),0.0),**kw):
""" Imports geometry from LSMGenGeo .geo file and creates spheres.
Since 2012 the package is available in Debian/Ubuntu and known as python-demgengeo
http://packages.qa.debian.org/p/python-demgengeo.html
:Parameters:
`filename`: string
file which has 4 colums [x, y, z, radius].
`shift`: Vector3
Vector3(X,Y,Z) parameter moves the specimen.
`scale`: float
factor scales the given data.
`orientation`: quaternion
orientation of the imported geometry
`**kw`: (unused keyword arguments)
is passed to :yref:`yade.utils.sphere`
:Returns: list of spheres.
LSMGenGeo library allows one to create pack of spheres
with given [Rmin:Rmax] with null stress inside the specimen.
Can be useful for Mining Rock simulation.
Example: :ysrc:`examples/packs/packs.py`, usage of LSMGenGeo library in :ysrc:`examples/test/genCylLSM.py`.
* https://answers.launchpad.net/esys-particle/+faq/877
* http://www.access.edu.au/lsmgengeo_python_doc/current/pythonapi/html/GenGeo-module.html
* https://svn.esscc.uq.edu.au/svn/esys3/lsm/contrib/LSMGenGeo/"""
from yade.utils import sphere
infile = open(fileName,"r")
lines = infile.readlines()
infile.close()
numSpheres = int(lines[6].split()[0])
ret=[]
for line in lines[7:numSpheres+7]:
data = line.split()
pos = orientation*Vector3(float(data[0]),float(data[1]),float(data[2]))
ret.append(utils.sphere(shift+scale*pos,scale*float(data[3]),**kw))
return ret
[docs]def gengeo(mntable,shift=Vector3.Zero,scale=1.0,**kw):
""" Imports geometry from LSMGenGeo library and creates spheres.
Since 2012 the package is available in Debian/Ubuntu and known as python-demgengeo
http://packages.qa.debian.org/p/python-demgengeo.html
:Parameters:
`mntable`: mntable
object, which creates by LSMGenGeo library, see example
`shift`: [float,float,float]
[X,Y,Z] parameter moves the specimen.
`scale`: float
factor scales the given data.
`**kw`: (unused keyword arguments)
is passed to :yref:`yade.utils.sphere`
LSMGenGeo library allows one to create pack of spheres
with given [Rmin:Rmax] with null stress inside the specimen.
Can be useful for Mining Rock simulation.
Example: :ysrc:`examples/packs/packs.py`, usage of LSMGenGeo library in :ysrc:`examples/test/genCylLSM.py`.
* https://answers.launchpad.net/esys-particle/+faq/877
* http://www.access.edu.au/lsmgengeo_python_doc/current/pythonapi/html/GenGeo-module.html
* https://svn.esscc.uq.edu.au/svn/esys3/lsm/contrib/LSMGenGeo/"""
try:
from GenGeo import MNTable3D,Sphere
except ImportError:
from gengeo import MNTable3D,Sphere
ret=[]
sphereList=mntable.getSphereListFromGroup(0)
for i in range(0, len(sphereList)):
r=sphereList[i].Radius()
c=sphereList[i].Centre()
ret.append(utils.sphere([shift[0]+scale*float(c.X()),shift[1]+scale*float(c.Y()),shift[2]+scale*float(c.Z())],scale*float(r),**kw))
return ret
[docs]def unv(fileName,shift=(0,0,0),scale=1.0,returnConnectivityTable=False,**kw):
""" Import geometry from unv file, return list of created facets.
:param string fileName: name of unv file
:param (float,float,float)|Vector3 shift: (X,Y,Z) parameter moves the specimen.
:param float scale: factor scales the given data.
:param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.facet`
:param bool returnConnectivityTable: if True, apart from facets returns also nodes (list of (x,y,z) nodes coordinates) and elements (list of (id1,id2,id3) element nodes ids). If False (default), returns only facets
unv files are mainly used for FEM analyses (are used by `OOFEM <http://www.oofem.org/>`_ and `Abaqus <http://www.simulia.com/products/abaqus_fea.html>`_), but triangular elements can be imported as facets.
These files cen be created e.g. with open-source free software `Salome <http://salome-platform.org>`_.
Example: :ysrc:`examples/test/unv-read/unvRead.py`."""
class UNVReader:
# class used in ymport.unv function
# reads and evaluate given unv file and extracts all triangles
# can be extended to read tetrahedrons as well
def __init__(self,fileName,shift=(0,0,0),scale=1.0,returnConnectivityTable=False,**kw):
self.shift = shift
self.scale = scale
self.unvFile = open(fileName,'r')
self.flag = 0
self.line = self.unvFile.readline()
self.lineSplit = self.line.split()
self.nodes = []
self.elements = []
self.read(**kw)
def readLine(self):
self.line = self.unvFile.readline()
self.lineSplit = self.line.split()
def read(self,**kw):
while self.line:
self.evalLine()
self.line = self.unvFile.readline()
self.unvFile.close()
self.createFacets(**kw)
def evalLine(self):
self.lineSplit = self.line.split()
if len(self.lineSplit) <= 1: # eval special unv format
if self.lineSplit[0] == '-1': pass
elif self.lineSplit[0] == '2411': self.flag = 1; # nodes
elif self.lineSplit[0] == '2412': self.flag = 2; # edges (lines)
else: self.flag = 4; # volume elements or other, not interesting for us (at least yet)
elif self.flag == 1: self.evalNodes()
elif self.flag == 2: self.evalEdge()
elif self.flag == 3: self.evalFacet()
#elif self.flag == 4: self.evalGroup()
def evalNodes(self):
self.readLine()
self.nodes.append((
self.shift[0]+self.scale*float(self.lineSplit[0]),
self.shift[1]+self.scale*float(self.lineSplit[1]),
self.shift[2]+self.scale*float(self.lineSplit[2])))
def evalEdge(self):
if self.lineSplit[1]=='41':
self.flag = 3
self.evalFacet()
else:
self.readLine()
self.readLine()
def evalFacet(self):
if self.lineSplit[1]=='41': # triangle
self.readLine()
self.elements.append((
int(self.lineSplit[0])-1,
int(self.lineSplit[1])-1,
int(self.lineSplit[2])-1))
else: # is not triangle
self.readLine()
self.flag = 4
# can be added function to handle tetrahedrons
def createFacets(self,**kw):
self.facets = [utils.facet(tuple(self.nodes[i] for i in e),**kw) for e in self.elements]
#
unvReader = UNVReader(fileName,shift,scale,returnConnectivityTable,**kw)
if returnConnectivityTable:
return unvReader.facets, unvReader.nodes, unvReader.elements
return facets
[docs]def iges(fileName,shift=(0,0,0),scale=1.0,returnConnectivityTable=False,**kw):
""" Import triangular mesh from .igs file, return list of created facets.
:param string fileName: name of iges file
:param (float,float,float)|Vector3 shift: (X,Y,Z) parameter moves the specimen.
:param float scale: factor scales the given data.
:param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.facet`
:param bool returnConnectivityTable: if True, apart from facets returns also nodes (list of (x,y,z) nodes coordinates) and elements (list of (id1,id2,id3) element nodes ids). If False (default), returns only facets
"""
nodes,elems = [],[]
f = open(fileName)
for line in f:
if line.startswith('134,'): # read nodes coordinates
ls = line.split(',')
v = Vector3(
float(ls[1])*scale + shift[0],
float(ls[2])*scale + shift[1],
float(ls[3])*scale + shift[2]
)
nodes.append(v)
if line.startswith('136,'): # read elements
ls = line.split(',')
i1,i2,i3 = int(ls[3])/2, int(ls[4])/2, int(ls[5])/2 # the numbering of nodes is 1,3,5,7,..., hence this int(ls[*])/2
elems.append( (i1,i2,i3) )
facets = [utils.facet( ( nodes[e[0]], nodes[e[1]], nodes[e[2]] ), **kw) for e in elems]
if returnConnectivityTable:
return facets, nodes, elems
return facets
[docs]def ele(nodeFileName,eleFileName,shift=(0,0,0),scale=1.0,**kw):
""" Import tetrahedral mesh from .ele file, return list of created tetrahedrons.
:param string nodeFileName: name of .node file
:param string eleFileName: name of .ele file
:param (float,float,float)|Vector3 shift: (X,Y,Z) parameter moves the specimen.
:param float scale: factor scales the given data.
:param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.polyhedron`
"""
f = open(nodeFileName)
line = f.readline()
while line.startswith('#'):
line = f.readline()
ls = line.split()
nVertices = int(ls[0])
if int(ls[1])!=3:
raise RuntimeError, "wrong .node file, number of dimensions should be 3"
vertices = [None for i in xrange(nVertices)]
shift = Vector3(shift)
for i in xrange(nVertices):
line = f.readline()
while line.startswith('#'):
line = f.readline()
ls = line.split()
if not ls:
continue
v = shift + scale*Vector3(tuple(float(ls[j]) for j in (1,2,3)))
vertices[int(ls[0])-1] = v
f.close()
#
f = open(eleFileName)
line = f.readline()
while line.startswith('#'):
line = f.readline()
ls = line.split()
if int(ls[1])!=4:
raise RuntimeError, "wrong .ele file, unsupported tetrahedra's number of nodes"
nTetras = int(ls[0])
tetras = [None for i in xrange(nTetras)]
for i in xrange(nTetras):
ls = f.readline().split()
tetras[int(ls[0])-1] = utils.polyhedron([vertices[int(ls[j])-1] for j in (1,2,3,4)],**kw)
f.close()
return tetras