Source code for yade.ymport

"""
Import geometry from various formats ('import' is python keyword, hence the name 'ymport').
"""

from builtins import range
from builtins import object
from yade.wrapper import *
from yade import utils

from yade.minieigenHP import *


[docs]def textExt(fileName,format='x_y_z_r',shift=Vector3.Zero,scale=1.0,attrs=[],**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`, 'x_y_z_r_attrs' :param [float,float,float] shift: [X,Y,Z] parameter moves the specimen. :param float scale: factor scales the given data. :param list attrs: attrs read from file if export.textExt(format='x_y_z_r_attrs') were used ('passed by refernece' style) :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)) elif (format=='x_y_z_r_attrs'): pos = Vector3(float(data[0]),float(data[1]),float(data[2])) s = utils.sphere(shift+scale*pos,scale*float(data[3]),**kw) ret.append(s) attrs.append(data[4:]) 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=Vector3.Zero,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,scale,scale) surf.translate(shift[0],shift[1],shift[2]) 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 easily be created with `GMSH <http://www.geuz.org/gmsh/>`_. Example added to :ysrc:`examples/packs/packs.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=[] elementlistVector3=[] # for deformable elements 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(object): # 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 unvReader.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 range(nVertices)] shift = Vector3(shift) for i in range(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 range(nTetras)] for i in range(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
[docs]def textPolyhedra(fileName,material,shift=Vector3.Zero,scale=1.0,orientation=Quaternion((0,1,0),0.0),**kw): """Load polyhedra from a text file. :param str filename: file name. Expected file format is the one output by export.textPolyhedra. :param [float,float,float] shift: [X,Y,Z] parameter moves the specimen. :param float scale: factor scales the given data. :param quaternion orientation: orientation of the imported polyhedra :param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.polyhedra_utils.polyhedra` :returns: list of polyhedras. Lines starting with # are skipped """ from yade import polyhedra_utils infile = open(fileName,"r") lines = infile.readlines() infile.close() ret=[] i=-1 while (i < (len(lines)-1)): i+=1 line = lines[i] data = line.split() if (data[0][0] == "#"): continue if (len(data)!=3): raise RuntimeError("Check polyhedra input file! Number of parameters in the first line is not 3!"); else: vertLoad = [] # ids = int(data[0]) verts = int(data[1]) surfs = int(data[2]) i+=1 for d in range(verts): dataV = lines[i].split() pos = orientation*Vector3(float(dataV[0])*scale,float(dataV[1])*scale,float(dataV[2])*scale)+shift vertLoad.append(pos) i+=1 polR = polyhedra_utils.polyhedra(material=material,v=vertLoad,**kw) if (polR != -1): ret.append(polR) i= i + surfs - 1 return ret