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------------------------------------------------------------
revno: 2949
committer: Bruno Chareyre <bruno.chareyre@xxxxxxxxxxx>
branch nick: trunk
timestamp: Mon 2011-10-31 18:43:05 +0100
message:
  - makeCloud can now generate spheres on a plane (see https://answers.launchpad.net/yade/+question/175606)
modified:
  pkg/dem/SpherePack.cpp
  py/pack/_packSpheres.cpp


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=== modified file 'pkg/dem/SpherePack.cpp'
--- pkg/dem/SpherePack.cpp	2011-05-02 18:49:39 +0000
+++ pkg/dem/SpherePack.cpp	2011-10-31 17:43:05 +0000
@@ -87,13 +87,14 @@
 	static boost::variate_generator<boost::minstd_rand&, boost::uniform_real<Real> > rnd(randGen, boost::uniform_real<Real>(0,1));
 	vector<Real> psdRadii; // holds plain radii (rather than diameters), scaled down in some situations to get the target number
 	vector<Real> psdCumm2; // psdCumm but dimensionally transformed to match mass distribution	
+	bool is2D = false;// Are we generating spheres alligned on a plane?
 	Vector3r size;
 	bool hSizeFound =(hSize!=Matrix3r::Zero());//is hSize passed to the function?
 	if (!hSizeFound) {size=mx-mn; hSize=size.asDiagonal();}
 	if (hSizeFound && !periodic) LOG_WARN("hSize can be defined only for periodic cells.");
 	Matrix3r invHsize =hSize.inverse();
 	Real volume=hSize.determinant();
-	if (!volume) throw invalid_argument("The box defined as null volume. Define at least maxCorner of the box, or hSize if periodic.");
+	if (!volume) LOG_WARN("The volume of the box is null, we will assume that the packing is 2D. If it is not what you want then you defined wrong input values; check that min and max corners are defined correctly.");
 	int mode=-1; bool err=false;
 	// determine the way we generate radii
 	if(porosity<=0) {LOG_WARN("porosity must be >0, changing it for you. It will be ineffective if rMean>0."); porosity=0.5;}
@@ -102,7 +103,16 @@
 	else if(num>0 && psdSizes.size()==0) {
 		mode=RDIST_NUM;
 		// the term (1+rRelFuzz²) comes from the mean volume for uniform distribution : Vmean = 4/3*pi*Rmean*(1+rRelFuzz²) 
-		rMean=pow(volume*(1-porosity)/(Mathr::PI*(4/3.)*(1+rRelFuzz*rRelFuzz)*num),1/3.);}
+		if (volume) rMean=pow(volume*(1-porosity)/(Mathr::PI*(4/3.)*(1+rRelFuzz*rRelFuzz)*num),1/3.);
+		else //The volume is null, we will generate a 2D packing with the following rMean
+		{
+			is2D=true;
+			size=mx-mn;
+			Real area=abs(size[0]*size[2]+size[0]*size[1]+size[1]*size[2]);//2 terms will be null if one coordinate is 0, the other is the area
+			if (!area) throw invalid_argument("The box defined as null volume AND null surface. Define at least maxCorner of the box, or hSize if periodic.");
+			rMean=pow(area*(1-porosity)/(Mathr::PI*(1+rRelFuzz*rRelFuzz)*num),0.5);
+		}
+	}
 	if(psdSizes.size()>0){
 		err=(mode>=0); mode=RDIST_PSD;
 		if(psdSizes.size()!=psdCumm.size()) throw invalid_argument(("SpherePack.makeCloud: psdSizes and psdCumm must have same dimensions ("+lexical_cast<string>(psdSizes.size())+"!="+lexical_cast<string>(psdCumm.size())).c_str());
@@ -134,7 +144,7 @@
 	if(err || mode<0) throw invalid_argument("SpherePack.makeCloud: at least one of rMean, porosity, psdSizes & psdCumm arguments must be specified. rMean can't be combined with psdSizes.");
 	// adjust uniform distribution parameters with distributeMass; rMean has the meaning (dimensionally) of _volume_
 	const int maxTry=1000;
-	if(periodic)(cellSize=size);
+// 	if(periodic)(cellSize=size);
 	Real r=0;
 	for(int i=0; (i<num) || (num<0); i++) {
 		Real norm, rand;
@@ -160,7 +170,7 @@
 		// try to put the sphere into a free spot
 		for(t=0; t<maxTry; ++t){
 			Vector3r c;
-			if(!periodic) { for(int axis=0; axis<3; axis++) c[axis]=mn[axis]+r+(size[axis]-2*r)*rnd(); }
+			if(!periodic) { for(int axis=0; axis<3; axis++) c[axis]=mn[axis]+(size[axis]?(size[axis]-2*r)*rnd()+r:0);}//we handle 2D with the special case size[axis]==0
 			else { 	for(int axis=0; axis<3; axis++) c[axis]=rnd();//coordinates in [0,1]
 				c=mn+hSize*c;}//coordinates in reference frame (inside the base cell)
 			size_t packSize=pack.size(); bool overlap=false;

=== modified file 'py/pack/_packSpheres.cpp'
--- py/pack/_packSpheres.cpp	2011-05-02 18:49:39 +0000
+++ py/pack/_packSpheres.cpp	2011-10-31 17:43:05 +0000
@@ -15,7 +15,7 @@
 		.def("load",&SpherePack::fromFile,(python::arg("fileName")),"Load packing from external text file (current data will be discarded).")
 		.def("save",&SpherePack::toFile,(python::arg("fileName")),"Save packing to external text file (will be overwritten).")
 		.def("fromSimulation",&SpherePack::fromSimulation,"Make packing corresponding to the current simulation. Discards current data.")
-		.def("makeCloud",&SpherePack::makeCloud,(python::arg("minCorner")=Vector3r(Vector3r::Zero()),python::arg("maxCorner")=Vector3r(Vector3r::Zero()),python::arg("rMean")=-1,python::arg("rRelFuzz")=0,python::arg("num")=-1,python::arg("periodic")=false,python::arg("porosity")=0.5,python::arg("psdSizes")=vector<Real>(),python::arg("psdCumm")=vector<Real>(),python::arg("distributeMass")=false,python::arg("seed")=0,python::arg("hSize")=Matrix3r(Matrix3r::Zero())),"Create random loose packing enclosed in a parallelepiped."
+		.def("makeCloud",&SpherePack::makeCloud,(python::arg("minCorner")=Vector3r(Vector3r::Zero()),python::arg("maxCorner")=Vector3r(Vector3r::Zero()),python::arg("rMean")=-1,python::arg("rRelFuzz")=0,python::arg("num")=-1,python::arg("periodic")=false,python::arg("porosity")=0.5,python::arg("psdSizes")=vector<Real>(),python::arg("psdCumm")=vector<Real>(),python::arg("distributeMass")=false,python::arg("seed")=0,python::arg("hSize")=Matrix3r(Matrix3r::Zero())),"Create random loose packing enclosed in a parallelepiped (also works in 2D if minCorner[k]=maxCorner[k] for one coordinate)."
 		"\nSphere radius distribution can be specified using one of the following ways:\n\n#. *rMean*, *rRelFuzz* and *num* gives uniform radius distribution in *rMean* (1 ± *rRelFuzz* ). Less than *num* spheres can be generated if it is too high.\n#. *rRelFuzz*, *num* and (optional) *porosity*, which estimates mean radius so that *porosity* is attained at the end.  *rMean* must be less than 0 (default). *porosity* is only an initial guess for the generation algorithm, which will retry with higher porosity until the prescibed *num* is obtained.\n#. *psdSizes* and *psdCumm*, two arrays specifying points of the `particle size distribution <http://en.wikipedia.org/wiki/Particle_size_distribution>`__ function. As many spheres as possible are generated.\n#. *psdSizes*, *psdCumm*, *num*, and (optional) *porosity*, like above but if *num* is not obtained, *psdSizes* will be scaled down uniformly, until *num* is obtained (see :yref:`appliedPsdScaling<yade._packSpheres.SpherePack.appliedPsdScaling>`).\n\nBy default (with ``distributeMass==False``), the distribution is applied to particle radii. The usual sense of \"particle size distribution\" is the distribution of *mass fraction* (rather than particle count); this can be achieved with ``distributeMass=True``."
 		"\n\nIf *num* is defined, then sizes generation is deterministic, giving the best fit of target distribution. It enables spheres placement in descending size order, thus giving lower porosity than the random generation."
 		"\n\n:param Vector3 minCorner: lower corner of an axis-aligned box\n:param Vector3 maxCorner: upper corner of an axis-aligned box\n:param Matrix3 hSize: base vectors of a generalized box (arbitrary parallelepiped, typically :yref:`Cell::hSize`), superseeds minCorner and maxCorner if defined. For periodic boundaries only.\n:param float rMean: mean radius or spheres\n:param float rRelFuzz: dispersion of radius relative to rMean\n:param int num: number of spheres to be generated. If negavite (default), generate as many as possible with stochastic sizes, ending after a fixed number of tries to place the sphere in space, else generate exactly *num* spheres with deterministic size distribution.\n:param bool periodic: whether the packing to be generated should be periodic\n:param float porosity: initial guess for the iterative generation procedure (if *num*>1). The algorithm will be retrying until the number of generated spheres is *num*. The first iteration tries with the provided porosity, but next iterations increase it if necessary (hence an initialy high porosity can speed-up the algorithm). If *psdSizes* is not defined, *rRelFuzz* ($z$) and *num* ($N$) are used so that the porosity given ($\\rho$) is approximately achieved at the end of generation, $r_m=\\sqrt[3]{\\frac{V(1-\\rho)}{\\frac{4}{3}\\pi(1+z^2)N}}$. The default is $\\rho$=0.5. The optimal value depends on *rRelFuzz* or  *psdSizes*.\n:param psdSizes: sieve sizes (particle diameters) when particle size distribution (PSD) is specified\n:param psdCumm: cummulative fractions of particle sizes given by *psdSizes*; must be the same length as *psdSizes* and should be non-decreasing\n:param bool distributeMass: if ``True``, given distribution will be used to distribute sphere's mass rather than radius of them.\n:param seed: number used to initialize the random number generator.\n:returns: number of created spheres, which can be lower than *num* depending on the method used.\n")