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Message #00765
[svn] r1565 - in trunk: gui/py lib/serialization pkg/dem/PreProcessor
Author: eudoxos
Date: 2008-10-29 20:29:18 +0100 (Wed, 29 Oct 2008)
New Revision: 1565
Modified:
trunk/gui/py/pyAttrUtils.hpp
trunk/lib/serialization/FundamentalHandler.tpp
trunk/lib/serialization/KnownFundamentalsHandler.tpp
trunk/pkg/dem/PreProcessor/MembraneTest.cpp
trunk/pkg/dem/PreProcessor/TriaxialTest.cpp
trunk/pkg/dem/PreProcessor/TriaxialTest.hpp
Log:
1. Make our intelligence-challenged deserializer finally gracefully handle nan, inf, -inf (arbitrary lower-upper case).
2. Fix crash in MembraneTest (leftover in the commit from testing, oh well)
3. Add TriaxialTest::fixedBoxDims to not scale selected box dimensions if sphere mean radius is given (example underway).
Modified: trunk/gui/py/pyAttrUtils.hpp
===================================================================
--- trunk/gui/py/pyAttrUtils.hpp 2008-10-29 10:31:21 UTC (rev 1564)
+++ trunk/gui/py/pyAttrUtils.hpp 2008-10-29 19:29:18 UTC (rev 1565)
@@ -4,6 +4,7 @@
#include<map>
#include<vector>
#include<boost/shared_ptr.hpp>
+#include<yade/lib-serialization/Archive.hpp>
#include<yade/lib-serialization-xml/XMLFormatManager.hpp>
#include<boost/python.hpp>
@@ -159,6 +160,7 @@
//! return python list of keys (attribute names)
boost::python::list pyKeys(){boost::python::list ret; for(DescriptorMap::iterator I=descriptors.begin();I!=descriptors.end();I++)ret.append(I->first); return ret;}
+
//! return attribute value as python object
boost::python::object pyGet(std::string key){
DescriptorMap::iterator I=descriptors.find(key);
@@ -167,15 +169,15 @@
LOG_DEBUG("Got raw attribute `"<<key<<"'");
switch(descriptors[key].type){
case BOOL: return python::object(lexical_cast<bool>(raw[0]));
- case NUMBER: return python::object(lexical_cast<double>(raw[0]));
+ case NUMBER: return python::object(lexical_cast_maybeNanInf<double>(raw[0]));
case STRING: return python::object(raw[0]);
case SEQ_STRING: {python::list ret; for(size_t i=0; i<raw.size(); i++) ret.append(python::object(raw[i])); return ret;}
- case SEQ_NUMBER: {python::list ret; for(size_t i=0; i<raw.size(); i++){ ret.append(python::object(lexical_cast<double>(raw[i]))); LOG_TRACE("Appended "<<raw[i]);} return ret; }
+ case SEQ_NUMBER: {python::list ret; for(size_t i=0; i<raw.size(); i++){ ret.append(python::object(lexical_cast_maybeNanInf<double>(raw[i]))); LOG_TRACE("Appended "<<raw[i]);} return ret; }
case VEC_VEC: {
python::list ret; for(size_t i=0; i<raw.size(); i++){
/* raw[i] has the form "{number number number}" */
vector<string> s; boost::algorithm::split(s,raw[i],algorithm::is_any_of("{} "),algorithm::token_compress_on);
- python::list subList; FOREACH(string ss, s) subList.append(python::object(lexical_cast<double>(ss)));
+ python::list subList; FOREACH(string ss, s) subList.append(python::object(lexical_cast_maybeNanInf<double>(ss)));
ret.append(subList);
}
}
Modified: trunk/lib/serialization/FundamentalHandler.tpp
===================================================================
--- trunk/lib/serialization/FundamentalHandler.tpp 2008-10-29 10:31:21 UTC (rev 1564)
+++ trunk/lib/serialization/FundamentalHandler.tpp 2008-10-29 19:29:18 UTC (rev 1565)
@@ -87,6 +87,15 @@
}
};
+template <typename RealType>
+RealType lexical_cast_maybeNanInf(const string& s){
+ if((s[0]=='n' || s[0]=='N') && (s[1]=='a' || s[1]=='A') && (s[2]=='n' || s[2]=='N')) return std::numeric_limits<RealType>::quiet_NaN();
+ if((s[0]=='i' || s[0]=='I') && (s[1]=='n' || s[1]=='N') && (s[2]=='f' || s[2]=='F')) return std::numeric_limits<RealType>::infinity();
+ if(s[0]=='-' && (s[1]=='i' || s[1]=='I') && (s[2]=='n' || s[2]=='N') && (s[3]=='f' || s[3]=='F')) return -std::numeric_limits<RealType>::infinity();
+ return lexical_cast<RealType>(s);
+};
+
+
template<typename Type >
inline void lexical_copy(Archive& ac , any& a )
{
@@ -99,7 +108,9 @@
try{
*tmp = lexical_cast<Type>(*tmpStr);
} catch(boost::bad_lexical_cast& e){
- if(typeid(tmp)==typeid(bool*) && atoi(tmpStr->c_str())!=0) { cerr<<"warning: offensive bool value `"<<*tmpStr<<"' encountered (interpreted as true)."<<endl; *tmp=lexical_cast<Type>("1"); /* cerr<<"New value: "<<lexical_cast<string>(*tmp)<<endl; cerr<<"Atoi returns "<<atoi(tmpStr->c_str())<<", bool !=0 is "<<(atoi(tmpStr->c_str())!=0)<<endl;*/ }
+ if(typeid(tmp)==typeid(bool*) && atoi(tmpStr->c_str())!=0) { cerr<<"warning: offensive bool value `"<<*tmpStr<<"' encountered (interpreted as true)."<<endl; *tmp=lexical_cast<Type>("1"); /* cerr<<"New value: "<<lexical_cast<string>(*tmp)<<endl; cerr<<"Atoi returns "<<atoi(tmpStr->c_str())<<", bool !=0 is "<<(atoi(tmpStr->c_str())!=0)<<endl;*/
+ }
+ else *tmp=lexical_cast_maybeNanInf<Type>(*tmpStr);
}
}
else if (a.type()==typeid(string*)) // serialization - writing to string from some Type
@@ -115,6 +126,9 @@
throw HandlerError(SerializationExceptions::LexicalCopyError);
}
+
+
+
template< >
struct FundamentalHandler< int >
{
Modified: trunk/lib/serialization/KnownFundamentalsHandler.tpp
===================================================================
--- trunk/lib/serialization/KnownFundamentalsHandler.tpp 2008-10-29 10:31:21 UTC (rev 1564)
+++ trunk/lib/serialization/KnownFundamentalsHandler.tpp 2008-10-29 19:29:18 UTC (rev 1565)
@@ -110,8 +110,8 @@
vector<string> tokens;
IOFormatManager::parseFundamental(*tmpStr, tokens);
- tmp->X() = lexical_cast<RealType>(tokens[0]);
- tmp->Y() = lexical_cast<RealType>(tokens[1]);
+ tmp->X() = lexical_cast_maybeNanInf<RealType>(tokens[0]);
+ tmp->Y() = lexical_cast_maybeNanInf<RealType>(tokens[1]);
}
else if (a.type()==typeid(const vector<unsigned char>*)) // from binary stream to Type
{
@@ -168,9 +168,9 @@
vector<string> tokens;
IOFormatManager::parseFundamental(*tmpStr, tokens);
- tmp->X() = lexical_cast<RealType>(tokens[0]);
- tmp->Y() = lexical_cast<RealType>(tokens[1]);
- tmp->Z() = lexical_cast<RealType>(tokens[2]);
+ tmp->X() = lexical_cast_maybeNanInf<RealType>(tokens[0]);
+ tmp->Y() = lexical_cast_maybeNanInf<RealType>(tokens[1]);
+ tmp->Z() = lexical_cast_maybeNanInf<RealType>(tokens[2]);
}
else if (a.type()==typeid(const vector<unsigned char>*)) // from binary stream to Type
{
@@ -231,10 +231,10 @@
vector<string> tokens;
IOFormatManager::parseFundamental(*tmpStr, tokens);
- tmp->X() = lexical_cast<RealType>(tokens[0]);
- tmp->Y() = lexical_cast<RealType>(tokens[1]);
- tmp->Z() = lexical_cast<RealType>(tokens[2]);
- tmp->W() = lexical_cast<RealType>(tokens[3]);
+ tmp->X() = lexical_cast_maybeNanInf<RealType>(tokens[0]);
+ tmp->Y() = lexical_cast_maybeNanInf<RealType>(tokens[1]);
+ tmp->Z() = lexical_cast_maybeNanInf<RealType>(tokens[2]);
+ tmp->W() = lexical_cast_maybeNanInf<RealType>(tokens[3]);
}
else if (a.type()==typeid(const vector<unsigned char>*)) // from binary stream to Type
{
@@ -299,10 +299,11 @@
vector<string> tokens;
IOFormatManager::parseFundamental(*tmpStr, tokens);
- *tmp = Matrix2<RealType>( lexical_cast<RealType>(tokens[0]),
- lexical_cast<RealType>(tokens[1]),
- lexical_cast<RealType>(tokens[2]),
- lexical_cast<RealType>(tokens[3]));
+ *tmp = Matrix2<RealType>(
+ lexical_cast_maybeNanInf<RealType>(tokens[0]),
+ lexical_cast_maybeNanInf<RealType>(tokens[1]),
+ lexical_cast_maybeNanInf<RealType>(tokens[2]),
+ lexical_cast_maybeNanInf<RealType>(tokens[3]));
}
else if (a.type()==typeid(const vector<unsigned char>*)) // from binary stream to Type
{
@@ -367,15 +368,16 @@
vector<string> tokens;
IOFormatManager::parseFundamental(*tmpStr, tokens);
- *tmp = Matrix3<RealType>( lexical_cast<RealType>(tokens[0]),
- lexical_cast<RealType>(tokens[1]),
- lexical_cast<RealType>(tokens[2]),
- lexical_cast<RealType>(tokens[3]),
- lexical_cast<RealType>(tokens[4]),
- lexical_cast<RealType>(tokens[5]),
- lexical_cast<RealType>(tokens[6]),
- lexical_cast<RealType>(tokens[7]),
- lexical_cast<RealType>(tokens[8]));
+ *tmp = Matrix3<RealType>(
+ lexical_cast_maybeNanInf<RealType>(tokens[0]),
+ lexical_cast_maybeNanInf<RealType>(tokens[1]),
+ lexical_cast_maybeNanInf<RealType>(tokens[2]),
+ lexical_cast_maybeNanInf<RealType>(tokens[3]),
+ lexical_cast_maybeNanInf<RealType>(tokens[4]),
+ lexical_cast_maybeNanInf<RealType>(tokens[5]),
+ lexical_cast_maybeNanInf<RealType>(tokens[6]),
+ lexical_cast_maybeNanInf<RealType>(tokens[7]),
+ lexical_cast_maybeNanInf<RealType>(tokens[8]));
}
else if (a.type()==typeid(const vector<unsigned char>*)) // from binary stream to Type
{
@@ -460,22 +462,23 @@
vector<string> tokens;
IOFormatManager::parseFundamental(*tmpStr, tokens);
- *tmp = Matrix4<RealType>( lexical_cast<RealType>(tokens[0]),
- lexical_cast<RealType>(tokens[1]),
- lexical_cast<RealType>(tokens[2]),
- lexical_cast<RealType>(tokens[3]),
- lexical_cast<RealType>(tokens[4]),
- lexical_cast<RealType>(tokens[5]),
- lexical_cast<RealType>(tokens[6]),
- lexical_cast<RealType>(tokens[7]),
- lexical_cast<RealType>(tokens[8]),
- lexical_cast<RealType>(tokens[9]),
- lexical_cast<RealType>(tokens[10]),
- lexical_cast<RealType>(tokens[11]),
- lexical_cast<RealType>(tokens[12]),
- lexical_cast<RealType>(tokens[13]),
- lexical_cast<RealType>(tokens[14]),
- lexical_cast<RealType>(tokens[15]));
+ *tmp = Matrix4<RealType>(
+ lexical_cast_maybeNanInf<RealType>(tokens[0]),
+ lexical_cast_maybeNanInf<RealType>(tokens[1]),
+ lexical_cast_maybeNanInf<RealType>(tokens[2]),
+ lexical_cast_maybeNanInf<RealType>(tokens[3]),
+ lexical_cast_maybeNanInf<RealType>(tokens[4]),
+ lexical_cast_maybeNanInf<RealType>(tokens[5]),
+ lexical_cast_maybeNanInf<RealType>(tokens[6]),
+ lexical_cast_maybeNanInf<RealType>(tokens[7]),
+ lexical_cast_maybeNanInf<RealType>(tokens[8]),
+ lexical_cast_maybeNanInf<RealType>(tokens[9]),
+ lexical_cast_maybeNanInf<RealType>(tokens[10]),
+ lexical_cast_maybeNanInf<RealType>(tokens[11]),
+ lexical_cast_maybeNanInf<RealType>(tokens[12]),
+ lexical_cast_maybeNanInf<RealType>(tokens[13]),
+ lexical_cast_maybeNanInf<RealType>(tokens[14]),
+ lexical_cast_maybeNanInf<RealType>(tokens[15]));
}
else if (a.type()==typeid(const vector<unsigned char>*)) // from binary stream to Type
{
@@ -594,17 +597,17 @@
if (tokens.size()==3) // Quaternion is written as axis which norm is the angle in radian
{
- axis[0] = lexical_cast<RealType>(tokens[0]);
- axis[1] = lexical_cast<RealType>(tokens[1]);
- axis[2] = lexical_cast<RealType>(tokens[2]);
+ axis[0] = lexical_cast_maybeNanInf<RealType>(tokens[0]);
+ axis[1] = lexical_cast_maybeNanInf<RealType>(tokens[1]);
+ axis[2] = lexical_cast_maybeNanInf<RealType>(tokens[2]);
angle = axis.Normalize();
}
else // tokens.size()==4 Quaternion is written as axis angle
{
- axis[0] = lexical_cast<RealType>(tokens[0]);
- axis[1] = lexical_cast<RealType>(tokens[1]);
- axis[2] = lexical_cast<RealType>(tokens[2]);
- angle = lexical_cast<RealType>(tokens[3]);
+ axis[0] = lexical_cast_maybeNanInf<RealType>(tokens[0]);
+ axis[1] = lexical_cast_maybeNanInf<RealType>(tokens[1]);
+ axis[2] = lexical_cast_maybeNanInf<RealType>(tokens[2]);
+ angle = lexical_cast_maybeNanInf<RealType>(tokens[3]);
}
tmp->FromAxisAngle(axis,angle);
}
@@ -687,23 +690,23 @@
if (tokens.size()==6) // Quaternion is written as axis which norm is the angle in radian
{
- position[0] = lexical_cast<RealType>(tokens[0]);
- position[1] = lexical_cast<RealType>(tokens[1]);
- position[2] = lexical_cast<RealType>(tokens[2]);
- axis[0] = lexical_cast<RealType>(tokens[4]);
- axis[1] = lexical_cast<RealType>(tokens[3]);
- axis[2] = lexical_cast<RealType>(tokens[5]);
+ position[0] = lexical_cast_maybeNanInf<RealType>(tokens[0]);
+ position[1] = lexical_cast_maybeNanInf<RealType>(tokens[1]);
+ position[2] = lexical_cast_maybeNanInf<RealType>(tokens[2]);
+ axis[0] = lexical_cast_maybeNanInf<RealType>(tokens[4]);
+ axis[1] = lexical_cast_maybeNanInf<RealType>(tokens[3]);
+ axis[2] = lexical_cast_maybeNanInf<RealType>(tokens[5]);
angle = axis.Normalize();
}
else // tokens.size()==7 Quaternion is writted as axis angle
{
- position[0] = lexical_cast<RealType>(tokens[0]);
- position[1] = lexical_cast<RealType>(tokens[1]);
- position[2] = lexical_cast<RealType>(tokens[2]);
- axis[0] = lexical_cast<RealType>(tokens[3]);
- axis[1] = lexical_cast<RealType>(tokens[4]);
- axis[2] = lexical_cast<RealType>(tokens[5]);
- angle = lexical_cast<RealType>(tokens[6]);
+ position[0] = lexical_cast_maybeNanInf<RealType>(tokens[0]);
+ position[1] = lexical_cast_maybeNanInf<RealType>(tokens[1]);
+ position[2] = lexical_cast_maybeNanInf<RealType>(tokens[2]);
+ axis[0] = lexical_cast_maybeNanInf<RealType>(tokens[3]);
+ axis[1] = lexical_cast_maybeNanInf<RealType>(tokens[4]);
+ axis[2] = lexical_cast_maybeNanInf<RealType>(tokens[5]);
+ angle = lexical_cast_maybeNanInf<RealType>(tokens[6]);
}
orientation.FromAxisAngle(axis,angle);
*tmp = Se3<RealType>(position,orientation);
Modified: trunk/pkg/dem/PreProcessor/MembraneTest.cpp
===================================================================
--- trunk/pkg/dem/PreProcessor/MembraneTest.cpp 2008-10-29 10:31:21 UTC (rev 1564)
+++ trunk/pkg/dem/PreProcessor/MembraneTest.cpp 2008-10-29 19:29:18 UTC (rev 1565)
@@ -301,7 +301,7 @@
//interactionGeometryDispatcher->add("InteractingMyTetrahedron2InteractingBox4InteractionOfMyTetrahedron");
shared_ptr<InteractingGeometryMetaEngine> interactingGeometryDispatcher = shared_ptr<InteractingGeometryMetaEngine>(new InteractingGeometryMetaEngine);
- //interactingGeometryDispatcher->add("ef2_BshTube_BssSweptSphereLineSegment_makeBssSweptSphereLineSegment");
+ interactingGeometryDispatcher->add("ef2_BshTube_BssSweptSphereLineSegment_makeBssSweptSphereLineSegment");
shared_ptr<BoundingVolumeMetaEngine> boundingVolumeDispatcher = shared_ptr<BoundingVolumeMetaEngine>(new BoundingVolumeMetaEngine);
boundingVolumeDispatcher->add("InteractingSphere2AABB"); //
Modified: trunk/pkg/dem/PreProcessor/TriaxialTest.cpp
===================================================================
--- trunk/pkg/dem/PreProcessor/TriaxialTest.cpp 2008-10-29 10:31:21 UTC (rev 1564)
+++ trunk/pkg/dem/PreProcessor/TriaxialTest.cpp 2008-10-29 19:29:18 UTC (rev 1565)
@@ -94,7 +94,7 @@
lowerCorner = Vector3r(0,0,0);
upperCorner = Vector3r(1,1,1);
thickness = 0.001;
- importFilename = "../../YADE/trunk-clean/examples/sphere16bidisperse.txt"; // "./small.sdec.xyz";
+ importFilename = ""; // oh, PLEASE, keep this empty -- i.e., by default, generate spheres in the box, not load them.
Key ="";
outputFileName = "./TriaxialTest"+Key+".xml";
//nlayers = 1;
@@ -260,6 +260,7 @@
REGISTER_ATTRIBUTE(DieCompaction);
REGISTER_ATTRIBUTE(translationspeed);
REGISTER_ATTRIBUTE(wishedporosity);
+ REGISTER_ATTRIBUTE(fixedBoxDims);
@@ -301,9 +302,13 @@
if(radiusMean<=0) really_radiusMean=pow(volume*(1-porosity)/(Mathr::PI*(4/3.)*numberOfGrains),1/3.);
else {
- Real boxScaleFactor=radiusMean*pow((4/3.)*Mathr::PI*numberOfGrains/(volume*(1-porosity)),1/3.);
- LOG_INFO("Mean radius value of "<<radiusMean<<" requested, scaling box by "<<boxScaleFactor);
- dimensions*=boxScaleFactor;
+ bool fixedDims[3];
+ fixedDims[0]=fixedBoxDims.find('x')!=string::npos; fixedDims[1]=fixedBoxDims.find('y')!=string::npos; fixedDims[2]=fixedBoxDims.find('z')!=string::npos;
+ int nScaled=(3-(int)fixedDims[0]+(int)fixedDims[1]+(int)fixedDims[2]);
+ if(nScaled==3) throw std::invalid_argument("At most 2 (not 3) axes can have fixed dimensions in fixedBoxDims if scaling for given radiusMean.");
+ Real boxScaleFactor=radiusMean*pow((4/3.)*Mathr::PI*numberOfGrains/(volume*(1-porosity)),1./nScaled);
+ LOG_INFO("Mean radius value of "<<radiusMean<<" requested, scaling "<<nScaled<<" dimensions by "<<boxScaleFactor);
+ dimensions[0]*=fixedDims[0]?1.:boxScaleFactor; dimensions[1]*=fixedDims[1]?1.:boxScaleFactor; dimensions[2]*=fixedDims[2]?1.:boxScaleFactor;
upperCorner=lowerCorner+dimensions;
really_radiusMean=radiusMean;
}
Modified: trunk/pkg/dem/PreProcessor/TriaxialTest.hpp
===================================================================
--- trunk/pkg/dem/PreProcessor/TriaxialTest.hpp 2008-10-29 10:31:21 UTC (rev 1564)
+++ trunk/pkg/dem/PreProcessor/TriaxialTest.hpp 2008-10-29 19:29:18 UTC (rev 1565)
@@ -120,7 +120,9 @@
string importFilename
,AnimationSnapshotsBaseName
,WallStressRecordFile
- ,Key;//A code that is added to output filenames
+ ,Key //A code that is added to output filenames
+ //! string that contains some subset (max. 2) of {'x','y','z'} ; containes axes will have box dimension hardcoded, even if box is scaled as mean_radius is prescribed: scaling will be applied on the rest.
+ ,fixedBoxDims;
shared_ptr<TriaxialCompressionEngine> triaxialcompressionEngine;
shared_ptr<TriaxialStressController> triaxialstressController;
