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------------------------------------------------------------
revno: 2980
committer: Bruno Chareyre <bruno.chareyre@xxxxxxxxxxx>
branch nick: trunk
timestamp: Wed 2011-12-07 22:01:08 +0100
message:
  - fix one bug mentionned in https://bugs.launchpad.net/yade/+bug/901146 (makeCloud with undefined num and psd)
  - more articles
modified:
  doc/yade-articles.bib
  pkg/dem/SpherePack.cpp


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=== modified file 'doc/yade-articles.bib'
--- doc/yade-articles.bib	2011-12-02 17:24:35 +0000
+++ doc/yade-articles.bib	2011-12-07 21:01:08 +0000
@@ -277,7 +277,8 @@
   title={Incrementally non-linear plasticity applied to rock joint modelling},
   author={Duriez, J. and Darve, F. and Donzé, F.V.},
   journal={International Journal for Numerical and Analytical Methods in Geomechanics},
-  year={2011}
+  year={2011},
+  doi = {10.1002/nag.1105}
 }
 
 @article{Donze2008,
@@ -312,4 +313,25 @@
   volume={2009},
   pages={P06012},
   year={2009}
-}
\ No newline at end of file
+}
+
+@article {Chareyre2011b,
+  author = {Chareyre, B. and Cortis, A. and Catalano, E. and Barthélemy, E.},
+  title = {Pore-Scale Modeling of Viscous Flow and Induced Forces in Dense Sphere Packings},
+  journal = {Transport in Porous Media},
+  publisher = {Springer Netherlands},
+  pages = {1-21},
+  url = {http://dx.doi.org/10.1007/s11242-011-9915-6},
+  doi = {10.1007/s11242-011-9915-6}
+}
+
+@Article{ Duriez2011,
+  author = {J. Duriez and F. Darve and F.-V. Donze},
+  title = {A discrete modeling-based constitutive relation for infilled rock joints},
+  year = {2011},
+  journal = {International Journal of Rock Mechanics \& Mining Sciences},
+  volume = {48},
+  number = {3},
+  pages = {458--468},
+  doi = {10.1016/j.ijrmms.2010.09.008}
+}

=== modified file 'pkg/dem/SpherePack.cpp'
--- pkg/dem/SpherePack.cpp	2011-11-02 15:09:47 +0000
+++ pkg/dem/SpherePack.cpp	2011-12-07 21:01:08 +0000
@@ -97,7 +97,7 @@
 	Matrix3r invHsize =hSize.inverse();
 	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 (!volume) {
-		if (hSizeFound || !periodic) throw invalid_argument("The box as null volume, this is not supported. One exception is for for flat box defined by min-max in periodic conditions, if hSize argument defines a non-null volume (or if the hSize argument is left undefined).");
+		if (hSizeFound || !periodic) throw invalid_argument("The box as null volume, this is not supported. One exception is for flat box defined by min-max in periodic conditions, if hSize argument defines a non-null volume (or if the hSize argument is left undefined).");
 		else LOG_WARN("The volume of the min-max 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
@@ -109,7 +109,7 @@
 		// the term (1+rRelFuzz²) comes from the mean volume for uniform distribution : Vmean = 4/3*pi*Rmean*(1+rRelFuzz²) 
 		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
-			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.");
+			if (!area) throw invalid_argument("The box defined has 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){
@@ -121,7 +121,7 @@
 		for(size_t i=0; i<psdSizes.size(); i++) {
 			psdRadii.push_back(/* radius, not diameter */ .5*psdSizes[i]);
 			if(distributeMass) {
-				//psdCumm2 is first obtained by integrating the number of particles over the volumic PSD (dN/dSize = totV*(dPassing/dSize)*1/(4/3πr³)). I suspect similar reasoning behind pow3Interp, since the expressions are a bit similar. The total cumulated number will be the number of spheres in volume*(1-porosity), it is used to decide if the PSD will be scaled down. psdCumm2 is normalized below in order to fit in [0,1]. (B.C.)
+				//psdCumm2 is first obtained by integrating the number of particles over the volumic PSD (dN/dSize = totV*(dPassing/dSize)*1/(4/3πr³)). The total cumulated number will be the number of spheres in volume*(1-porosity), it is used to decide if the PSD will be scaled down. psdCumm2 is normalized below in order to fit in [0,1]. (Bruno C.)
 				if (i==0) psdCumm2.push_back(0);
 				else psdCumm2.push_back(psdCumm2[i-1] + 3.0* (volume?volume:(area*psdSizes[psdSizes.size()-1])) *(1-porosity)/Mathr::PI*(psdCumm[i]-psdCumm[i-1])/(psdSizes[i]-psdSizes[i-1])*(pow(psdSizes[i-1],-2)-pow(psdSizes[i],-2)));
 			}
@@ -129,11 +129,13 @@
 			// check monotonicity
 			if(i>0 && (psdSizes[i-1]>psdSizes[i] || psdCumm[i-1]>psdCumm[i])) throw invalid_argument("SpherePack:makeCloud: psdSizes and psdCumm must be both non-decreasing.");
 		}
-		// check the consistency between sizes, num, and poro. If target number will not fit in (1-poro)*volume, scale down particles sizes
+		//Normalize psdCumm2 so it's between 0 and 1
+		if(distributeMass) for(size_t i=1; i<psdSizes.size(); i++) psdCumm2[i]/=psdCumm2[psdSizes.size()-1];
+		
+		// check the consistency between sizes, num, and poro if all three are imposed. If target number will not fit in (1-poro)*volume, scale down particles sizes
 		if (num>1){
 			appliedPsdScaling=1;
 			if(distributeMass) {
-				
 				if (psdCumm2[psdSizes.size()-1]<num) appliedPsdScaling=pow(psdCumm2[psdSizes.size()-1]/num,1./3.);
 				//Normalize psdCumm2 so it's between 0 and 1
 				for(size_t i=1; i<psdSizes.size(); i++) psdCumm2[i]/=psdCumm2[psdSizes.size()-1];