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/////////////////////////////////////////////////////////////
// //
// Copyright (c) 2007-2017 by The University of Queensland //
// Centre for Geoscience Computing //
// http://earth.uq.edu.au/centre-geoscience-computing //
// //
// Primary Business: Brisbane, Queensland, Australia //
// Licensed under the Open Software License version 3.0 //
// http://www.apache.org/licenses/LICENSE-2.0 //
// //
/////////////////////////////////////////////////////////////
#include <boost/version.hpp>
#include <iostream>
#include <fstream>
#include <sstream>
#include "MNTable3DPy.h"
using namespace std;
using namespace boost::python;
using boost::python::arg;
void exportMNTable3D()
{
// Disable autogeneration of C++ signatures (Boost 1.34.0 and higher)
// for Epydoc which stumbles over indentation in the automatically generated strings.
boost::python::docstring_options no_autogen(true,false);
class_<MNTable3D>(
"MNTable3D",
"A multi-group neighbour table for constructing 3D particle assemblies",
init<>()
)
.def(init<const MNTable3D &>())
.def(
init<Vector3&,Vector3&,double, unsigned int>(
( boost::python::arg("minPoint"), boost::python::arg("maxPoint"), boost::python::arg("gridSize"), boost::python::arg("numGroups")=1 ),
"Constructs a neighbour table with specified bounds, cell size and initial number of particle groups.\n"
"@type minPoint: L{Vector3}\n"
"@kwarg minPoint: front-lower-left point of the particle region\n"
"@type maxPoint: L{Vector3}\n"
"@kwarg maxPoint: back-upper-right point of the particle region\n"
"@type gridSize: double\n"
"@kwarg gridSize: the cell size for neighbour searches\n"
"@type numGroups: unsigned int\n"
"@kwarg numGroups: the initial number of groups (default: 1)\n"
)
)
.def(
"insertFromRawFile",
&MNTable3D::insertFromRawFile,
( boost::python::arg("fileName"), boost::python::arg("scale"), boost::python::arg("tolerance") ),
"Reads in an existing geometry from a file in a raw ASCII format\n"
"@type fileName: string\n"
"@kwarg fileName: the name of the raw ASCII geometry file to read\n"
"@type scale: double\n"
"@kwarg scale: a scaling factor to apply to coordinates and radius\n"
"@type tolerance: double\n"
"@kwarg tolerance: the tolerance for determining whether particles collide\n"
)
.def(
"tagParticlesInSphere",
&MNTable3D::tagParticlesInSphere,
( boost::python::arg("sphere"), boost::python::arg("tag"), boost::python::arg("groupID")=0 ),
"Assigns the specified tag to all particles from group C{groupID} "
"that lie within the given L{Sphere}.\n"
"@type sphere: L{Sphere}\n"
"@kwarg sphere: the sphere within which to tag particles\n"
"@type tag: int\n"
"@kwarg tag: the tag to assign particles\n"
"@type groupID: unsigned int\n"
"@kwarg groupID: the group ID of particles to tag (default: 0)\n"
"@rtype: void\n"
)
.def(
"tagParticlesAlongPlane",
&MNTable3D::tagParticlesAlongPlane,
( boost::python::arg("plane"), boost::python::arg("distance"), boost::python::arg("tag"), boost::python::arg("groupID")=0 ),
"Assigns the specified tag to all particles from group C{groupID} "
"that lie within the specified distance of the given L{Plane}.\n"
"@type plane: L{Plane}\n"
"@kwarg plane: the plane along which to tag particles\n"
"@type distance: double\n"
"@kwarg distance: the maximum distance between tagged particles and the plane\n"
"@type tag: int\n"
"@kwarg tag: the tag to assign particles\n"
"@type groupID: unsigned int\n"
"@kwarg groupID: the group ID of particles to tag (default: 0)\n"
"@rtype: void\n"
)
.def(
"tagParticlesInVolume",
&MNTable3D::tagParticlesInVolume,
( boost::python::arg("volume"), boost::python::arg("tag"), boost::python::arg("groupID")=0 ),
"Assigns the specified tag to all particles within the specified L{AVolume3D} from group C{groupID}\n"
"that lie within the specified volume.\n"
"@type volume: L{AVolume3D}\n"
"@kwarg volume: the volume within which to tag particles\n"
"@type tag: int\n"
"@kwarg tag: the tag to assign particles\n"
"@type groupID: unsigned int\n"
"@kwarg groupID: the group ID of particles to tag (default: 0)\n"
"@rtype: void\n"
)
.def(
"tagParticlesAlongPlaneWithMask",
&MNTable3D::tagParticlesAlongPlaneWithMask,
( boost::python::arg("plane"), boost::python::arg("distance"), boost::python::arg("tag"),boost::python::arg("mask"), boost::python::arg("groupID")=0 ),
"Assigns the specified tag to all particles from group C{groupID} "
"that lie within the specified distance of a given L{Plane}."
" Use of tag masks is permitted.\n"
"@type plane: L{Plane}\n"
"@kwarg plane: the plane along which to tag particles\n"
"@type distance: double\n"
"@kwarg distance: the maximum distance between tagged particles and the plane\n"
"@type tag: int\n"
"@kwarg tag: the tag to assign particles\n"
"@type mask: int\n"
"@kwarg mask: the mask determining which bits of the tag are used\n"
"@type groupID: unsigned int\n"
"@kwarg groupID: the group ID of particles to tag (default: 0)\n"
"@rtype: void\n"
)
.def(
"tagParticlesAlongJoints",
&MNTable3D::tagParticlesAlongJoints,
( boost::python::arg("jointset"), boost::python::arg("distance"), boost::python::arg("tag"),boost::python::arg("mask"), boost::python::arg("groupID")=0 ),
"Assigns the specified tag to all particles from group C{groupID} "
"that lie within the specified distance of a given L{TriPatchSet}\n"
"@type joints: L{TriPatchSet}\n"
"@kwarg joints: the set of triangular patches along which to tag particles\n"
"@type distance: double\n"
"@kwarg distance: the maximum distance between tagged particles and the triangles in the L{TriPatchSet}\n"
"@type tag: int\n"
"@kwarg tag: the tag to assign particles\n"
"@type mask: int\n"
"@kwarg mask: the mask determining which bits of the tag are used\n"
"@type groupID: unsigned int\n"
"@kwarg groupID: the group ID of particles to tag (default: 0)\n"
"@rtype: void\n"
)
.def(
"removeParticlesWithTag",
&MNTable3D::removeParticlesWithTag,
( boost::python::arg("tag"), boost::python::arg("groupID")=0 ),
"Removes all particles with the specified tag from a given group\n"
"@type tag: int\n"
"@kwarg tag: the tag of particles to remove\n"
"@type groupID: unsigned int\n"
"@kwarg groupID: the group ID of particles to remove (default: 0)\n"
"@rtype: void\n"
)
.def(
"removeTaggedParticles",
&MNTable3D::removeParticlesWithTagMask,
(boost::python::arg("groupID")=0, boost::python::arg("tag"), boost::python::arg("mask")),
"Removes all particles with a specified tag from a given group\n"
"@type groupID: unsigned int\n"
"@kwarg groupID: the group ID of particles to remove (default: 0)\n"
"@type tag: int\n"
"@kwarg tag: the tag of particles to remove\n"
"@type mask: int\n"
"@kwarg mask: the mask determining which bits of the tag are used\n"
"@rtype: void\n"
)
.def(
"removeParticlesInVolume",
&MNTable3D::removeParticlesInVolume,
(boost::python::arg("volume"), boost::python::arg("groupID")=0, boost::python::arg("full")),
"Removes all particles inside the specified L{AVolume3D}\n"
"@type volume: L{AVolume3D}\n"
"@kwarg volume: the volume within which to remove particles\n"
"@type groupID: unsigned int\n"
"@kwarg groupID: the group ID of particles to remove (default: 0)\n"
"@type full: bool\n"
"@kwarg full: remove particles fully inside volume or only with centres inside the volume\n"
)
.def(
"removeParticlesInGroup",
&MNTable3D::removeParticlesInGroup,
( boost::python::arg("groupID") ),
"Removes all particles from a given group\n"
"@type groupID: unsigned int\n"
"@kwarg groupID: the group ID of particles to remove \n"
"@rtype: void\n"
)
.def(
"renumberParticlesContinuous",
&MNTable3D::renumberParticlesContinuous,
"Changes all particle IDs so that they are continuous "
"i.e. 0,1,..,Np-1\n"
)
.def(
"generateBonds",
&MNTable3D::generateBonds,
(boost::python::arg("groupID")=0, boost::python::arg("tolerance"), boost::python::arg("bondID") ),
"Generates bonds between particle pairs separated by less than the specified tolerance\n"
"@type groupID: int\n"
"@kwarg groupID: the group ID of particles to bond together (default: 0)\n"
"@type tolerance: double\n"
"@kwarg tolerance: maximum distance separating bonded particles\n"
"@type bondID: int\n"
"@kwarg bondID: the bond ID to assign generated bonds\n"
"@rtype: void\n"
)
.def(
"generateBondsTagged",
&MNTable3D::generateBondsTagged,
(boost::python::arg("groupID")=0, boost::python::arg("tolerance"), boost::python::arg("bondID"), boost::python::arg("particleTag1"), boost::python::arg("particleTag2") ),
"Generates bonds between particle pairs with the two specified tags.\n"
"@type groupID: int\n"
"@kwarg groupID: the group ID of particles to bond together (default: 0)\n"
"@type tolerance: double\n"
"@kwarg tolerance: maximum distance separating bonded particles\n"
"@type bondID: int\n"
"@kwarg bondID: the bond ID to assign generated bonds\n"
"@type particleTag1: int\n"
"@kwarg particleTag1: the first tag of particles to bond\n"
"@type particleTag2: int\n"
"@kwarg particleTag2: the second tag of particles to bond\n"
"@rtype: void\n"
)
.def(
"generateRandomBonds",
&MNTable3D::generateRandomBonds,
(boost::python::arg("groupID")=0, boost::python::arg("tolerance"), boost::python::arg("probability"), boost::python::arg("bondID"), boost::python::arg("particleTag"), boost::python::arg("tagMask") ),
"Generates bonds between particle pairs. Bonds will be created with a specified probability <= 1\n"
"@type groupID: int\n"
"@kwarg groupID: the group ID of particles to bond together (default: 0)\n"
"@type tolerance: double\n"
"@kwarg tolerance: maximum distance separating bonded particles\n"
"@type probability: double\n"
"@kwarg probability: the probability that a bond will be generated (0 < probability <= 1)\n"
"@type bondID: int\n"
"@kwarg bondID: the bond ID to assign generated bonds\n"
"@type particleTag: int\n"
"@kwarg particleTag: the tag of particles to bond\n"
"@type tagMask: int\n"
"@kwarg tagMask: the mask determining which bits of the tag are used\n"
"@rtype: void\n"
)
.def(
"generateBondsWithJointSet",
&MNTable3D::generateBondsWithJointSet,
(boost::python::arg("JointSet"), boost::python::arg("groupID")=0, boost::python::arg("tolerance"), boost::python::arg("bondTag") ),
"Generates bonds between particle pairs, checking whether the bond crosses a specified L{TriPatchSet} representing joints.\n"
"A bond that crosses a triangle will be assigned a bondTag equal to the tag of the triangle.\n"
"A bond that does not cross any triangle will be assigned a bondTag equal to the supplied bondTag.\n"
"@type JointSet: L{TriPatchSet}\n"
"@kwarg JointSet: Set of triangles to check for crossing bonds\n"
"@type groupID: int\n"
"@kwarg groupID: the group ID of particles to bond together (default: 0)\n"
"@type tolerance: double\n"
"@kwarg tolerance: maximum distance separating bonded particles\n"
"@type bondTag: int\n"
"@kwarg bondTag: the bond tag to assign to bonds that do not cross a joint (DO NOT set this equal to the tag of any triangle contained in the joint set).\n"
"@rtype: void\n"
)
.def(
"generateClusterBonds",
&MNTable3D::generateClusterBonds,
(boost::python::arg("groupID")=0, boost::python::arg("tolerance"), boost::python::arg("bondTag1"), boost::python::arg("bondTag2")),
"Generates bonds with different tags depending on whether the particle tags are the same or different.\n"
"@type groupID: int\n"
"@kwarg groupID: the group ID of particles to bond together (default: 0)\n"
"@type tolerance: double\n"
"@kwarg tolerance: maximum distance separating bonded particles\n"
"@type bondTag1: int\n"
"@kwarg bondTag1: the bond tag to assign for bonds joining particles of the same tag\n"
"@type bondTag2: int\n"
"@kwarg bondTag2: the bond tag to assign for bonds joining particles of differing tag\n"
)
.def(
"getSumVolume",
&MNTable3D::getSumVolume,
( boost::python::arg("groupID")=0 ),
"Returns the sum of the particle volumes in the specified group.\n"
"@type groupID: int\n"
"@kwarg groupID: the group ID of particles whose volumes are summed (default: 0).\n"
"@rtype: double\n"
)
.def(
"getSphereListFromGroup",
&MNTable3D::getSphereListFromGroup,
( boost::python::arg("groupID")=0 ),
"Returns a python list of L{Sphere} objects with the specified group ID\n"
"@type groupID: int\n"
"@kwarg groupID: the group ID of spheres to return as a list (default: 0)\n"
"@rtype: boost::python::list\n"
)
.def(
"getSphereListDist",
&MNTable3D::getSphereListDist,
( boost::python::arg("posn"),boost::python::arg("dist"),boost::python::arg("groupID")=0 ),
"Returns a python list of L{Sphere} objects within a defined distance \n"
"of the specified point\n"
"@type posn: L{Vector3}\n"
"@kwarg posn: the location of the point\n"
"@type dist: double\n"
"@kwarg dist: the distance from the point to particles that will be returned\n"
"@type groupID: int\n"
"@kwarg groupID: the group ID of spheres to return as a list (default: 0)\n"
"@rtype: boost::python::list\n"
)
.def(
"GrowNGroups",
&MNTable3D::GrowNGroups,
( boost::python::arg("numGroups") ),
"Expands the neighbour table to permit the specified number of particle groups\n"
"@type numGroups: int\n"
"@kwarg numGroups: number of groups to create\n"
"@rtype: void\n"
)
.def(
"write",
&MNTable3D::write,
( boost::python::arg("fileName"), boost::python::arg("outputStyle") ),
"Writes the particle assembly and bonding information to the specified\n"
"file using the specified output style (0: debug; 1: geo; 2: vtk)\n"
"@type fileName: string\n"
"@kwarg fileName: the name of the file to write\n"
"@type outputStyle: int\n"
"@kwarg outputStyle: output style (0: debug; 1: geo; 2: vtk)\n"
"@rtype: void\n"
)
.def(
"tagParticlesInGroup",
&MNTable3D::tagParticlesInGroupNT,
(boost::python::arg("groupID")=0, boost::python::arg("tag") ),
"Tag all particles with the specified C{groupID}\n"
"@type groupID: int\n"
"@kwarg groupID: the group ID of particles to tag (default: 0)\n"
"@type tag: int\n"
"@kwarg tag: the tag to be assigned to the selected particles\n"
)
.def(
"tagParticlesInGroup",
&MNTable3D::tagParticlesInGroup,
(boost::python::arg("groupID")=0, boost::python::arg("tag"), boost::python::arg("mask") ),
"@type mask: int\n"
"@kwarg mask: only the bits which are 1 in the mask are actually\n"
" changed in the tag (optional)\n"
"@rtype: void\n"
)
.def(
"tagParticlesToClosest",
&MNTable3D::tagParticlesToClosest,
( boost::python::arg("groupID1")=0, boost::python::arg("groupID2") ),
"Tags particles in C{groupID1} closest to spheres in C{groupID2}.\n"
"The particle ID of C{groupID2} specifies the tag assigned to nearest particles in C{groupID1}.\n"
"@type groupID1: int\n"
"@kwarg groupID1: the group ID of particles to tag (default: 0).\n"
"@type groupID2: int\n"
"@kwarg groupID2: the group ID of closest spheres.\n"
)
.def(
"tagParticlesToClosestAnisotropic",
&MNTable3D::tagParticlesToClosestAnisotropic,
( boost::python::arg("groupID1")=0, boost::python::arg("groupID2"), boost::python::arg("wx"), boost::python::arg("wy"), boost::python::arg("wz") ),
"Tags particles in C{groupID1} closest to spheres in C{groupID2} using distance weighting factors for aniostropic particle cluster shapes.\n"
"The particle ID of C{groupID2} specifies the tag assigned to nearest particles in C{groupID1}.\n"
"@type groupID1: int\n"
"@kwarg groupID1: the group ID of particles to tag (default: 0).\n"
"@type groupID2: int\n"
"@kwarg groupID2: the group ID of closest spheres.\n"
"@type wx: double\n"
"@kwarg wx: the weighting of the x-component of the distance.\n"
"@type wy: double\n"
"@kwarg wy: the weighting of the y-component of the distance.\n"
"@type wz: double\n"
"@kwarg wz: the weighting of the z-component of the distance.\n"
)
.def(
"insert",
&MNTable3D::insert,
( boost::python::arg("sphere"), boost::python::arg("groupID")=0 ),
"Inserts sphere\n"
"@type sphere: L{Sphere}\n"
"@kwarg sphere: the sphere to insert\n"
"@type groupID: int\n"
"@kwarg groupID: the group ID of the inserted sphere (default: 0).\n"
)
.def(
"insertBond",
&MNTable3D::insertBond,
( boost::python::arg("Id1"), boost::python::arg("Id2"), boost::python::arg("tag") ),
"Inserts bond between particles with the specified particle IDs\n"
"@type Id1: int\n"
"@kwarg Id1: ID of first particle to bond\n"
"@type Id2: int\n"
"@kwarg Id2: ID of second particle to bond\n"
"@type tag: int\n"
"@kwarg tag: the bond tag to assign to the generated bond\n"
)
.def(
"setOutputPrecision",
&MNTable3D::SetOutputPrecision,
( boost::python::arg("precision")),
"Set the number of significant digits for file output\n"
"@type precision: int\n"
"@kwarg precision: the number of significant digits (default: 10).\n"
)
.def(
"initBlockWriting",
&MNTable3D::initBlockWriting,
( boost::python::arg("filename")),
"Initialize data needed for blocked writing\n"
"@type filename: string\n"
"@kwarg filename: The name of the geo file to be written.\n"
)
.def(
"writeBlock",
&MNTable3D::writeBlock,
( boost::python::arg("minPoint"), boost::python::arg("maxPoint")),
"Write particles in block to already initialized file\n"
"@type minPoint: Vector3\n"
"@kwarg minPoint: The minimum point of the block.\n"
"@type maxPoint: Vector3\n"
"@kwarg maxPoint: The maximum point of the block.\n"
)
.def(
"writeBondsBlocked",
&MNTable3D::writeBondsBlocked,
"Writing the current bonds to a temporary file.\n"
)
.def(
"removeBonds",
&MNTable3D::removeBonds,
"Delete all currently stored bonds.\n"
)
.def(
"finishBlockWriting",
&MNTable3D::finishBlockWriting,
"Finish block writing.\n"
)
.def(self_ns::str(self))
;
}
|
