// 2007,2008 © Václav Šmilauer <eudoxos@arcig.cz>

#include <lib/base/AliasNamespaces.hpp>
#include <lib/base/Logging.hpp>
#include <lib/pyutil/doc_opts.hpp>
#include <lib/pyutil/gil.hpp>
#include <lib/pyutil/raw_constructor.hpp>
#include <lib/serialization/ObjectIO.hpp>
#include <core/Clump.hpp>
#include <core/EnergyTracker.hpp>
#include <core/FileGenerator.hpp>
#include <core/Functor.hpp>
#include <core/GlobalEngine.hpp>
#include <core/Omega.hpp>
#include <core/PartialEngine.hpp>
#include <core/ThreadRunner.hpp>
#include <core/Timing.hpp>
#include <pkg/common/Collider.hpp>
#include <pkg/common/Dispatching.hpp>
#include <pkg/common/InteractionLoop.hpp>
#include <pkg/common/KinematicEngines.hpp>
#include <pkg/common/ParallelEngine.hpp>
#include <pkg/common/Sphere.hpp>
#include <pkg/dem/LubricationWithPotential.hpp>
#include <pkg/dem/STLImporter.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/archive/codecvt_null.hpp>
#include <boost/bind.hpp>
#include <boost/lambda/bind.hpp>
#include <boost/math/special_functions/nonfinite_num_facets.hpp>
#include <boost/python/raw_function.hpp>
#include <boost/random/linear_congruential.hpp>
#include <boost/random/uniform_real.hpp>
#include <boost/random/variate_generator.hpp>
#include <csignal>
#include <locale>

#ifdef YADE_MPI
#include <core/Subdomain.hpp>
#endif

CREATE_CPP_LOCAL_LOGGER("yadeWrapper.cpp");

namespace yade { // Cannot have #include directive inside.

/*
Python normally iterates over object it is has __getitem__ and __len__, which BodyContainer does.
However, it will not skip removed bodies automatically, hence this iterator which does just that.
*/
class pyBodyIterator {
	BodyContainer::iterator I, Iend;

public:
	pyBodyIterator(const shared_ptr<BodyContainer>& bc)
	{
		I    = bc->begin();
		Iend = bc->end();
	}
	pyBodyIterator   pyIter() { return *this; }
	shared_ptr<Body> pyNext()
	{
		BodyContainer::iterator ret;
		while (I != Iend) {
			ret = I;
			++I;
			if (*ret)
				return *ret;
		}
		PyErr_SetNone(PyExc_StopIteration);
		py::throw_error_already_set(); /* never reached, but makes the compiler happier */
		throw;
	}
};

class pyBodyContainer {
private:
	void checkClump(shared_ptr<Body> b)
	{
		if (!(b->isClump())) {
			PyErr_SetString(PyExc_TypeError, ("Error: Body" + boost::lexical_cast<string>(b->getId()) + " is not a clump.").c_str());
			py::throw_error_already_set();
		}
	}
	typedef std::map<Body::id_t, Se3r> MemberMap;

public:
	const shared_ptr<BodyContainer> proxee;
	pyBodyIterator                  pyIter() { return pyBodyIterator(proxee); }
	pyBodyContainer(const shared_ptr<BodyContainer>& _proxee)
	        : proxee(_proxee)
	{
	}
	// raw access to the underlying
	bool getUseRedirection(void) { return proxee->useRedirection; }
	bool getEnableRedirection(void) { return proxee->enableRedirection; }
	void setUseRedirection(bool val)
	{
		if (val and not proxee->useRedirection == val)
			proxee->useRedirection = val;
		proxee->dirty = true;
		if (val)
			proxee->enableRedirection = true;
	}
	void setEnableRedirection(bool val)
	{
		proxee->enableRedirection = val;
		if (not val)
			proxee->useRedirection = false;
	}

	shared_ptr<Body> pyGetitem(Body::id_t _id)
	{
		int id = (_id >= 0 ? _id : proxee->size() + _id);
		if (id < 0 || (size_t)id >= proxee->size()) {
			PyErr_SetString(PyExc_IndexError, "Body id out of range.");
			py::throw_error_already_set(); /* make compiler happy; never reached */
			return shared_ptr<Body>();
		} else
			return (*proxee)[id];
	}
	Body::id_t append(shared_ptr<Body> b)
	{
		// shoud be >=0, but Body is by default created with id 0... :-|
		if (b->getId() >= 0) {
			PyErr_SetString(
			        PyExc_IndexError,
			        ("Body already has id " + boost::lexical_cast<string>(b->getId())
			         + " set; appending such body (for the second time) is not allowed.")
			                .c_str());
			py::throw_error_already_set();
		}
		return proxee->insert(b);
	}
	Body::id_t         insertAtId(shared_ptr<Body> b, Body::id_t pos) { return proxee->insertAtId(b, pos); }
	vector<Body::id_t> appendList(vector<shared_ptr<Body>> bb)
	{
		boost::mutex::scoped_lock lock(Omega::instance().renderMutex);
		vector<Body::id_t>        ret;
		FOREACH(shared_ptr<Body> & b, bb) { ret.push_back(append(b)); }
		return ret;
	}
	Body::id_t clump(vector<Body::id_t> ids, unsigned int discretization)
	{
		// create and add clump itself
		Scene*            scene(Omega::instance().getScene().get());
		shared_ptr<Body>  clumpBody = shared_ptr<Body>(new Body());
		shared_ptr<Clump> clump     = shared_ptr<Clump>(new Clump());
		clumpBody->shape            = clump;
		clumpBody->setBounded(false);
		proxee->insert(clumpBody);
		// add clump members to the clump
		FOREACH(Body::id_t id, ids)
		{
			if (Body::byId(id, scene)->isClumpMember()) {                                                 //Check, whether the body is clumpMember
				Clump::del(Body::byId(Body::byId(id, scene)->clumpId, scene), Body::byId(id, scene)); //If so, remove it from there
			}
		};

		FOREACH(Body::id_t id, ids) Clump::add(clumpBody, Body::byId(id, scene));
		Clump::updateProperties(clumpBody, discretization);
		return clumpBody->getId();
	}
	py::tuple appendClump(vector<shared_ptr<Body>> bb, unsigned int discretization)
	{
		// append constituent particles
		vector<Body::id_t> ids(appendList(bb));
		// clump them together (the clump fcn) and return
		return py::make_tuple(clump(ids, discretization), ids);
	}
	void updateClumpProperties(py::list excludeList, unsigned int discretization)
	{
		//convert excludeList to a c++ list
		vector<Body::id_t> excludeListC;
		for (int ii = 0; ii < py::len(excludeList); ii++)
			excludeListC.push_back(py::extract<Body::id_t>(excludeList[ii])());
		for (const auto& b : *proxee) {
			if (!(std::find(excludeListC.begin(), excludeListC.end(), b->getId()) != excludeListC.end())) {
				if (b->isClump())
					Clump::updateProperties(b, discretization);
			}
		}
	}
	void deleteClumpMember(shared_ptr<Body> clumpBody, shared_ptr<Body> memberBody)
	{ //FIXME
		const shared_ptr<Clump> clump(YADE_PTR_CAST<Clump>(clumpBody->shape));
		if (clump->members.size() == 1) {
			Clump::del(clumpBody, memberBody); //phD was not commented out
			for (unsigned i = 0; i < clump->ids.size(); i++) {
				if (clump->ids[i] == memberBody->getId()) {
					clump->ids.erase(clump->ids.begin() + i);
				}
			}
			proxee->erase(memberBody->getId(), false);
			proxee->erase(clumpBody->getId(), false);

		} else {
			Clump::del(clumpBody, memberBody); //pHD was not commented out
			for (unsigned i = 0; i < clump->ids.size(); i++) {
				if (clump->ids[i] == memberBody->getId()) {
					clump->ids.erase(clump->ids.begin() + i);
				}
			}
			Clump::updatePropertiesNonSpherical(clumpBody, /*intersecting*/ false);
			proxee->erase(memberBody->getId(), false);
		}
	}
	void deleteClumpBody(shared_ptr<Body> clumpBody)
	{ //FIXME
		const shared_ptr<Clump> clump(YADE_PTR_CAST<Clump>(clumpBody->shape));

		//if (clump->members.size()==0 ){
		//	proxee->erase(clumpBody->getId());
		//}else{
		Scene* scene(Omega::instance().getScene().get());
		int    totalNumber = clump->ids.size();
		int    count       = 0;
		while (count < totalNumber) {
			//for (int i=0; i<clump->ids.size(); i++){
			shared_ptr<Body> memberBody(YADE_PTR_CAST<Body>(Body::byId(clump->ids[/*i */ 0], scene)));
			deleteClumpMember(clumpBody, memberBody);
			//clump->ids.erase(clump->ids.begin()+i);
			//proxee->erase(memberBody->getId());
			count++;
		}

		proxee->erase(clumpBody->getId(), true);
		//}
	}
	void addToClump(vector<Body::id_t> bids, Body::id_t cid, unsigned int discretization)
	{
		Scene*           scene(Omega::instance().getScene().get()); // get scene
		shared_ptr<Body> clp = Body::byId(cid, scene);              // get clump pointer
		checkClump(clp);
		vector<Body::id_t> eraseList;
		FOREACH(Body::id_t bid, bids)
		{
			shared_ptr<Body> bp = Body::byId(bid, scene); // get body pointer
			if (bp->isClump()) {
				if (bp == clp) {
					PyErr_Warn(
					        PyExc_UserWarning,
					        ("Warning: Body " + boost::lexical_cast<string>(bid) + " and clump " + boost::lexical_cast<string>(cid)
					         + " are the same bodies. Body was not added.")
					                .c_str());
					return;
				}
				Clump::add(clp, bp); //add clump bid to clump cid
				eraseList.push_back(bid);
			} else if (bp->isClumpMember()) {
				Body::id_t       bpClumpId      = bp->clumpId;
				shared_ptr<Body> bpClumpPointer = Body::byId(bpClumpId, scene);
				if (bpClumpPointer == clp) {
					PyErr_Warn(
					        PyExc_UserWarning,
					        ("Warning: Body " + boost::lexical_cast<string>(bid) + " is already a clump member of clump "
					         + boost::lexical_cast<string>(cid) + ". Body was not added.")
					                .c_str());
					return;
				}
				Clump::add(clp, bpClumpPointer); //add clump bpClumpId to clump cid
				eraseList.push_back(bpClumpId);
			} else
				Clump::add(clp, bp); // bp must be a standalone!
		}
		Clump::updateProperties(clp, discretization);
		FOREACH(Body::id_t bid, eraseList) proxee->erase(bid, false); //erase old clumps
	}
	void releaseFromClump(Body::id_t bid, Body::id_t cid, unsigned int discretization)
	{
		Scene*           scene(Omega::instance().getScene().get()); // get scene
		shared_ptr<Body> bp  = Body::byId(bid, scene);              // get body pointer
		shared_ptr<Body> clp = Body::byId(cid, scene);              // get clump pointer
		checkClump(clp);
		if (bp->isClumpMember()) {
			Body::id_t bpClumpId = bp->clumpId;
			if (cid == bpClumpId) {
				const shared_ptr<Clump>&    clump   = YADE_PTR_CAST<Clump>(clp->shape);
				std::map<Body::id_t, Se3r>& members = clump->members;
				if (members.size() == 2) {
					PyErr_Warn(
					        PyExc_UserWarning,
					        ("Warning: Body " + boost::lexical_cast<string>(bid) + " not released from clump "
					         + boost::lexical_cast<string>(cid) + ", because number of clump members would get < 2!")
					                .c_str());
					return;
				}
				Clump::del(clp, bp); //release bid from cid
				Clump::updateProperties(clp, discretization);
			} else {
				PyErr_Warn(
				        PyExc_UserWarning,
				        ("Warning: Body " + boost::lexical_cast<string>(bid) + " must be a clump member of clump "
				         + boost::lexical_cast<string>(cid) + ". Body was not released.")
				                .c_str());
				return;
			}
		} else {
			PyErr_Warn(
			        PyExc_UserWarning,
			        ("Warning: Body " + boost::lexical_cast<string>(bid) + " is not a clump member. Body was not released.").c_str());
			return;
		}
	}
	py::list replaceByClumps(py::list ctList, vector<Real> amounts, unsigned int discretization)
	{
		py::list ret;
		Real     checkSum = 0.0;
		FOREACH(Real amount, amounts)
		{
			if (amount < 0.0) {
				PyErr_SetString(PyExc_ValueError, ("Error: One or more of given amounts are negative!"));
				py::throw_error_already_set();
			} else
				checkSum += amount;
		}
		if (checkSum > 1.0) {
			PyErr_SetString(
			        PyExc_ValueError,
			        ("Error: Sum of amounts " + boost::lexical_cast<string>(checkSum) + " should not be bigger than 1.0!").c_str());
			py::throw_error_already_set();
		}
		if (py::len(ctList) != (unsigned)amounts.size()) { //avoid unsigned comparison warning
			PyErr_SetString(
			        PyExc_ValueError,
			        ("Error: Length of amounts list (" + boost::lexical_cast<string>(amounts.size()) + ") differs from length of template list ("
			         + boost::lexical_cast<string>(py::len(ctList)) + ").")
			                .c_str());
			py::throw_error_already_set();
		}
		//set a random generator (code copied from pkg/dem/SpherePack.cpp):
		static boost::minstd_rand randGen((int)TimingInfo::getNow(/* get the number even if timing is disabled globally */ true));
		typedef boost::variate_generator<boost::minstd_rand&, boost::uniform_real<>> UniRandGen;
		static UniRandGen                                                            rndUnit(randGen, boost::uniform_real<>(-1, 1));

		//get number of spherical particles and a list of all spheres:
		vector<shared_ptr<Body>> sphereList;
		shared_ptr<Sphere>       sph(new Sphere);
		int                      Sph_Index = sph->getClassIndexStatic();
		for (const auto& b : *proxee)
			if ((b->shape->getClassIndex() == Sph_Index) && (b->isStandalone()))
				sphereList.push_back(b);
		int num = sphereList.size();

		//loop over templates:
		int numSphereList = num, numTemplates = amounts.size();
		for (int ii = 0; ii < numTemplates; ii++) {
			//ctList: [<ct1>,<ct2>, ...] = [<int,[double,double, ... ],[Vector3r,Vector3r, ...]>,<int,[double,double, ... ],[Vector3r,Vector3r, ...]>, ...]
			//ct: <len(relRadList),relRadList,relPosList> = <int,[double,double, ... ],[Vector3r,Vector3r, ...]> (python objects)
			//relRadList: [relRad1,relRad2, ...] (list of doubles)
			//relPosList: [relPos1,relPos2, ...] (list of vectors)

			//extract attributes from python objects:
			py::object ctTmp         = ctList[ii];
			int        numCM         = py::extract<int>(ctTmp.attr("numCM"))(); // number of clump members
			py::list   relRadListTmp = py::extract<py::list>(ctTmp.attr("relRadii"))();
			py::list   relPosListTmp = py::extract<py::list>(ctTmp.attr("relPositions"))();

			//get relative radii and positions; calculate volumes; get balance point: get axis aligned bounding box; get minimum radius;
			vector<Real>     relRadTmp(numCM), relVolTmp(numCM);
			vector<Vector3r> relPosTmp(numCM);
			Vector3r         relPosTmpMean = Vector3r::Zero();
			Real             rMin          = 1. / 0.;
			AlignedBox3r     aabb;
			for (int jj = 0; jj < numCM; jj++) {
				relRadTmp[jj] = py::extract<Real>(relRadListTmp[jj])();
				relVolTmp[jj] = (4. / 3.) * Mathr::PI * pow(relRadTmp[jj], 3.);
				relPosTmp[jj] = py::extract<Vector3r>(relPosListTmp[jj])();
				relPosTmpMean += relPosTmp[jj];
				aabb.extend(relPosTmp[jj] + Vector3r::Constant(relRadTmp[jj]));
				aabb.extend(relPosTmp[jj] - Vector3r::Constant(relRadTmp[jj]));
				rMin = min(rMin, relRadTmp[jj]);
			}
			relPosTmpMean /= numCM; //balance point

			//get volume of the clump template using regular cubic cell array inside axis aligned bounding box of the clump:
			//(some parts are duplicated from intergration algorithm in Clump::updateProperties)
			Real     dx = rMin / 5.;     //edge length of cell
			Real     dv = pow(dx, 3);    //volume of a single cell
			Vector3r x;                  //position vector (center) of cell
			Real     relVolSumTmp = 0.0; //volume of clump template
			for (x.x() = aabb.min().x() + dx / 2.; x.x() < aabb.max().x(); x.x() += dx) {
				for (x.y() = aabb.min().y() + dx / 2.; x.y() < aabb.max().y(); x.y() += dx) {
					for (x.z() = aabb.min().z() + dx / 2.; x.z() < aabb.max().z(); x.z() += dx) {
						for (int jj = 0; jj < numCM; jj++) {
							if ((x - relPosTmp[jj]).squaredNorm() < pow(relRadTmp[jj], 2)) {
								relVolSumTmp += dv;
								break;
							}
						}
					}
				}
			}

			//get pointer lists of spheres, that should be replaced:
			int                      numReplaceTmp = int(std::round(num * amounts[ii]));
			vector<shared_ptr<Body>> bpListTmp(numReplaceTmp);
			int                      a = 0, c = 0; //counters
			vector<int>              posTmp;
			FOREACH(const shared_ptr<Body>& b, sphereList)
			{
				if (c == a * numSphereList / numReplaceTmp) {
					bpListTmp[a] = b;
					a++;
					posTmp.push_back(c); //remember position in sphereList
				}
				c++;
			}
			for (int jj = 0; jj < a; jj++) {
				sphereList.erase(sphereList.begin() + posTmp[jj] - jj); //remove bodies from sphereList, that were already found
				numSphereList--;
			}

			//adapt position- and radii-informations and replace spheres from bpListTmp by clumps:
			FOREACH(const shared_ptr<Body>& b, bpListTmp)
			{
				//get sphere, that should be replaced:
				const Sphere*        sphere = YADE_CAST<Sphere*>(b->shape.get());
				shared_ptr<Material> matTmp = b->material;

				//get a random rotation quaternion:
				Quaternionr randAxisTmp = (Quaternionr)AngleAxisr(2 * Mathr::PI * rndUnit(), Vector3r(rndUnit(), rndUnit(), rndUnit()));
				randAxisTmp.normalize();

				//convert geometries in global coordinates (scaling):
				Real               scalingFactorVolume = ((4. / 3.) * Mathr::PI * pow(sphere->radius, 3.)) / relVolSumTmp;
				Real               scalingFactor1D     = pow(scalingFactorVolume, 1. / 3.); //=((vol. sphere)/(relative clump volume))^(1/3)
				vector<Vector3r>   newPosTmp(numCM);
				vector<Real>       newRadTmp(numCM);
				vector<Body::id_t> idsTmp(numCM);
				for (int jj = 0; jj < numCM; jj++) {
					newPosTmp[jj] = relPosTmp[jj] - relPosTmpMean;   //shift position, to get balance point at (0,0,0)
					newPosTmp[jj] = randAxisTmp * newPosTmp[jj];     //rotate around balance point
					newRadTmp[jj] = relRadTmp[jj] * scalingFactor1D; //scale radii
					newPosTmp[jj] = newPosTmp[jj] * scalingFactor1D; //scale position
					newPosTmp[jj] += b->state->pos;                  //translate new position to spheres center

					//create spheres:
					shared_ptr<Body> newSphere    = shared_ptr<Body>(new Body());
					newSphere->state->blockedDOFs = State::DOF_NONE;
					newSphere->state->mass = scalingFactorVolume * relVolTmp[jj] * matTmp->density; //vol. corrected mass for clump members
					Real inertiaTmp        = 2.0 / 5.0 * newSphere->state->mass * newRadTmp[jj] * newRadTmp[jj];
					newSphere->state->inertia = Vector3r(inertiaTmp, inertiaTmp, inertiaTmp);
					newSphere->state->pos     = newPosTmp[jj];
					newSphere->material       = matTmp;

					shared_ptr<Sphere> sphereTmp = shared_ptr<Sphere>(new Sphere());
					sphereTmp->radius            = newRadTmp[jj];
					sphereTmp->color             = Vector3r(Mathr::UnitRandom(), Mathr::UnitRandom(), Mathr::UnitRandom());
					sphereTmp->color.normalize();
					newSphere->shape = sphereTmp;

					shared_ptr<Aabb> aabbTmp = shared_ptr<Aabb>(new Aabb());
					aabbTmp->color           = Vector3r(0, 1, 0);
					newSphere->bound         = aabbTmp;
					proxee->insert(newSphere);
					LOG_DEBUG("New body (sphere) " << newSphere->id << " added.");
					idsTmp[jj] = newSphere->id;
				}
				Body::id_t newClumpId = clump(idsTmp, discretization);
				ret.append(py::make_tuple(newClumpId, idsTmp));
				erase(b->id, false);
			}
		}
		return ret;
	}
	Real getRoundness(py::list excludeList)
	{
		Scene*             scene(Omega::instance().getScene().get()); // get scene
		shared_ptr<Sphere> sph(new Sphere);
		int                Sph_Index = sph->getClassIndexStatic(); // get sphere index for checking if bodies are spheres
		//convert excludeList to a c++ list
		vector<Body::id_t> excludeListC;
		for (int ii = 0; ii < py::len(excludeList); ii++)
			excludeListC.push_back(py::extract<Body::id_t>(excludeList[ii])());
		Real RC_sum = 0.0; //sum of local roundnesses
		Real R1, R2, vol, dens;
		int  c = 0; //counter
		for (const auto& b : *proxee) {
			if (!(std::find(excludeListC.begin(), excludeListC.end(), b->getId()) != excludeListC.end())) {
				if ((b->shape->getClassIndex() == Sph_Index) && (b->isStandalone())) {
					RC_sum += 1.0;
					c += 1;
				}
				if (b->isClump()) {
					R2                                  = 0.0;
					dens                                = 0.0;
					vol                                 = 0.0;
					const shared_ptr<Clump>&    clump   = YADE_PTR_CAST<Clump>(b->shape);
					std::map<Body::id_t, Se3r>& members = clump->members;
					for (MemberMap::value_type& mm : members) {
						const Body::id_t&       memberId = mm.first;
						const shared_ptr<Body>& member   = Body::byId(memberId, scene);
						assert(member->isClumpMember());
						if (member->shape->getClassIndex() == Sph_Index) { //clump member should be a sphere
							const Sphere* sphere = YADE_CAST<Sphere*>(member->shape.get());
							R2
							        = max((member->state->pos - b->state->pos).norm() + sphere->radius,
							              R2); //get minimum radius of a sphere, that imbeds clump
							dens = member->material->density;
						}
					}
					if (dens > 0.)
						vol = b->state->mass / dens;
					R1 = pow((3. * vol) / (4. * Mathr::PI), 1. / 3.); //get theoretical radius of a sphere, with same volume as clump
					if (R2 < R1) {
						PyErr_Warn(PyExc_UserWarning, ("Something went wrong in getRoundness method (R2 < R1 detected)."));
						return 0;
					}
					RC_sum += R1 / R2;
					c += 1;
				}
			}
		}
		if (c == 0)
			c = 1;     //in case no spheres and no clumps are present in the scene: RC = 0
		return RC_sum / c; //return roundness coefficient RC
	}
	vector<Body::id_t> replace(vector<shared_ptr<Body>> bb)
	{
		proxee->clear();
		return appendList(bb);
	}
	long length() { return proxee->size(); }
	void clear() { proxee->clear(); }
	bool erase(Body::id_t id, bool eraseClumpMembers) { return proxee->erase(id, eraseClumpMembers); }
#ifdef YADE_MPI
	vector<Body::id_t> subdomainBodies() { return proxee->subdomainBodies; }
#endif
};


class pyTags {
public:
	pyTags(const shared_ptr<Scene> _mb)
	        : mb(_mb)
	{
	}
	const shared_ptr<Scene> mb;
	bool                    hasKey(const string& key)
	{
		FOREACH(string val, mb->tags)
		{
			if (boost::algorithm::starts_with(val, key + "=")) {
				return true;
			}
		}
		return false;
	}
	string getItem(const string& key)
	{
		FOREACH(string & val, mb->tags)
		{
			if (boost::algorithm::starts_with(val, key + "=")) {
				string val1(val);
				boost::algorithm::erase_head(val1, key.size() + 1);
				return val1;
			}
		}
		PyErr_SetString(PyExc_KeyError, ("Invalid key: " + key + ".").c_str());
		py::throw_error_already_set(); /* make compiler happy; never reached */
		return string();
	}
	void setItem(const string& key, const string& item)
	{
		if (key.find("=") != string::npos) {
			PyErr_SetString(PyExc_KeyError, "Key must not contain the '=' character (implementation limitation; sorry).");
			py::throw_error_already_set();
		}
		FOREACH(string & val, mb->tags)
		{
			if (boost::algorithm::starts_with(val, key + "=")) {
				val = key + "=" + item;
				return;
			}
		}
		mb->tags.push_back(key + "=" + item);
	}
	py::list keys()
	{
		py::list ret;
		FOREACH(string val, mb->tags)
		{
			size_t i = val.find("=");
			if (i == string::npos)
				throw runtime_error("Tags must be in the key=value format (internal error?)");
			boost::algorithm::erase_tail(val, val.size() - i);
			ret.append(val);
		}
		return ret;
	}
};


class pyInteractionIterator {
	InteractionContainer::iterator I, Iend;

public:
	pyInteractionIterator(const shared_ptr<InteractionContainer>& ic)
	{
		I    = ic->begin();
		Iend = ic->end();
	}
	pyInteractionIterator   pyIter() { return *this; }
	shared_ptr<Interaction> pyNext()
	{
		InteractionContainer::iterator ret;
		while (I != Iend) {
			ret = I;
			++I;
			if ((*ret)->isReal())
				return *ret;
		}
		PyErr_SetNone(PyExc_StopIteration);
		py::throw_error_already_set();
		throw;  // to avoid compiler warning; never reached
		        // InteractionContainer::iterator ret=I; ++I; return *ret;
	}
};

class pyInteractionContainer {
public:
	const shared_ptr<InteractionContainer> proxee;
	const shared_ptr<Scene>                scene;
	pyInteractionContainer(const shared_ptr<InteractionContainer>& _proxee)
	        : proxee(_proxee)
	        , scene(Omega::instance().getScene())
	{
	}
	pyInteractionIterator   pyIter() { return pyInteractionIterator(proxee); }
	bool                    has(Body::id_t id1, Body::id_t id2) { return proxee->found(id1, id2); }
	shared_ptr<Interaction> pyGetitem(vector<Body::id_t> id12)
	{
		//if(!PySequence_Check(id12.ptr())) throw invalid_argument("Key must be a tuple");
		//if(py::len(id12)!=2) throw invalid_argument("Key must be a 2-tuple: id1,id2.");
		if (id12.size() == 2) {
			//if(max(id12[0],id12[1])>
			shared_ptr<Interaction> i = proxee->find(id12[0], id12[1]);
			if (i)
				return i;
			else {
				PyErr_SetString(PyExc_IndexError, "No such interaction");
				py::throw_error_already_set(); /* make compiler happy; never reached */
				return shared_ptr<Interaction>();
			}
		} else if (id12.size() == 1) {
			return (*proxee)[id12[0]];
		} else
			throw invalid_argument("2 integers (id1,id2) or 1 integer (nth) required.");
	}
	/* return nth _real_ iteration from the container (0-based index); this is to facilitate picking random interaction */
	shared_ptr<Interaction> pyNth(long n)
	{
		long i = 0;
		FOREACH(shared_ptr<Interaction> I, *proxee)
		{
			if (!I->isReal())
				continue;
			if (i++ == n)
				return I;
		}
		PyErr_SetString(
		        PyExc_IndexError,
		        (string("Interaction number out of range (") + boost::lexical_cast<string>(n) + ">=" + boost::lexical_cast<string>(i) + ").").c_str());
		py::throw_error_already_set(); /* make compiler happy; never reached */
		return shared_ptr<Interaction>();
	}
	long     len() { return proxee->size(); }
	void     clear() { proxee->clear(); }
	py::list withBody(long id)
	{
		py::list ret;
		FOREACH(const Body::MapId2IntrT::value_type& I, Body::byId(id, scene)->intrs)
		{
			if (I.second->isReal())
				ret.append(I.second);
		}
		return ret;
	}
	py::list withBodyAll(long id)
	{
		py::list ret;
		FOREACH(const Body::MapId2IntrT::value_type& I, Body::byId(id, scene)->intrs) ret.append(I.second);
		return ret;
	}
	py::list getAll(bool onlyReal)
	{
		py::list ret;
		FOREACH(const shared_ptr<Interaction>& I, *proxee)
		{
			if (onlyReal && !I->isReal())
				continue;
			ret.append(I);
		}
		return ret;
	}
	long countReal()
	{
		long ret = 0;
		FOREACH(const shared_ptr<Interaction>& I, *proxee)
		{
			if (I->isReal())
				ret++;
		}
		return ret;
	}
	bool serializeSorted_get() { return proxee->serializeSorted; }
	void serializeSorted_set(bool ss) { proxee->serializeSorted = ss; }
	void eraseNonReal() { proxee->eraseNonReal(); }
	void erase(Body::id_t id1, Body::id_t id2) { proxee->requestErase(id1, id2); }
};

class pyForceContainer {
	shared_ptr<Scene> scene;

public:
	pyForceContainer(shared_ptr<Scene> _scene)
	        : scene(_scene)
	{
	}
	void checkId(long id)
	{
		if (id < 0 || (size_t)id >= scene->bodies->size()) {
			PyErr_SetString(PyExc_IndexError, "Body id out of range.");
			py::throw_error_already_set(); /* never reached */
			throw;
		}
	}
	Vector3r force_get(long id, bool sync)
	{
		checkId(id);
		if (!sync and !scene->forces.synced)
			return scene->forces.getForceSingle(id);
		scene->forces.sync();
		return scene->forces.getForce(id);
	}
	Vector3r torque_get(long id, bool sync)
	{
		checkId(id);
		if (!sync and !scene->forces.synced)
			return scene->forces.getTorqueSingle(id);
		scene->forces.sync();
		return scene->forces.getTorque(id);
	}
	void force_add(long id, const Vector3r& f, bool permanent)
	{
		checkId(id);
		if (!permanent)
			scene->forces.addForce(id, f);
		else {
			LOG_WARN("O.forces.addF(...,permanent=True) is deprecated, use O.forces.setPermF(...) instead");
			scene->forces.setPermForce(id, f);
		}
	}
	void torque_add(long id, const Vector3r& t, bool permanent)
	{
		checkId(id);
		if (!permanent)
			scene->forces.addTorque(id, t);
		else {
			LOG_WARN("O.forces.addT(...,permanent=True) is deprecated, use O.forces.setPermT(...) instead");
			scene->forces.setPermTorque(id, t);
		}
	}
	Vector3r permForce_get(long id)
	{
		checkId(id);
		return scene->forces.getPermForce(id);
	}
	Vector3r permTorque_get(long id)
	{
		checkId(id);
		return scene->forces.getPermTorque(id);
	}
	void permForce_set(long id, const Vector3r& f)
	{
		checkId(id);
		scene->forces.setPermForce(id, f);
	}
	void permTorque_set(long id, const Vector3r& t)
	{
		checkId(id);
		scene->forces.setPermTorque(id, t);
	}
	void reset(bool resetAll) { scene->forces.reset(scene->iter, resetAll); }
	long syncCount_get() { return scene->forces.syncCount; }
	void syncCount_set(long count) { scene->forces.syncCount = count; }
	bool getPermForceUsed() { return scene->forces.getPermForceUsed(); }
};

class pyMaterialContainer {
	shared_ptr<Scene> scene;

public:
	pyMaterialContainer(shared_ptr<Scene> _scene)
	        : scene(_scene)
	{
	}
	shared_ptr<Material> getitem_id(int _id)
	{
		int id = (_id >= 0 ? _id : scene->materials.size() + _id);
		if (id < 0 || (size_t)id >= scene->materials.size()) {
			PyErr_SetString(PyExc_IndexError, "Material id out of range.");
			py::throw_error_already_set(); /* never reached */
			throw;
		}
		return Material::byId(id, scene);
	}
	shared_ptr<Material> getitem_label(string label)
	{
		// translate runtime_error to KeyError (instead of RuntimeError) if the material doesn't exist
		try {
			return Material::byLabel(label, scene);
		} catch (std::runtime_error& e) {
			PyErr_SetString(PyExc_KeyError, e.what());
			py::throw_error_already_set(); /* never reached; avoids warning */
			throw;
		}
	}
	int append(shared_ptr<Material> m)
	{
		scene->materials.push_back(m);
		m->id = scene->materials.size() - 1;
		return m->id;
	}
	vector<int> appendList(vector<shared_ptr<Material>> mm)
	{
		vector<int> ret;
		FOREACH(shared_ptr<Material> & m, mm) ret.push_back(append(m));
		return ret;
	}
	int len() { return (int)scene->materials.size(); }
	int index(const std::string& label) { return Material::byLabelIndex(label, scene.get()); }
};

void termHandlerNormal(int /*sig*/)
{
	cerr << "Yade: normal exit." << endl;
	raise(SIGTERM);
}
void termHandlerError(int /*sig*/)
{
	cerr << "Yade: error exit." << endl;
	raise(SIGTERM);
}

class pyOmega {
private:
	// can be safely removed now, since pyOmega makes an empty scene in the constructor, if there is none
	void assertScene()
	{
		if (!OMEGA.getScene())
			throw std::runtime_error("No Scene instance?!");
	}
	Omega& OMEGA;

public:
	pyOmega()
	        : OMEGA(Omega::instance())
	{
		shared_ptr<Scene> rb = OMEGA.getScene();
		if (!rb) {
			OMEGA.init();
			rb = OMEGA.getScene();
		}
		assert(rb);
		if (!OMEGA.hasSimulationLoop()) {
			OMEGA.createSimulationLoop();
		}
	};
	/* Create variables in python's __builtin__ namespace that correspond to labeled objects. At this moment, only engines and functors can be labeled (not bodies etc). */
	void mapLabeledEntitiesToVariables()
	{
// not sure if we should map materials to variables by default...
// a call to this functions would have to be added to pyMaterialContainer::append
#if 0
			FOREACH(const shared_ptr<Material>& m, OMEGA.getScene()->materials){
				if(!m->label.empty()) { PyGILState_STATE gstate; gstate = PyGILState_Ensure(); PyRun_SimpleString(("__builtins__."+m->label+"=Omega().materials["+boost::lexical_cast<string>(m->id)+"]").c_str()); PyGILState_Release(gstate); }
			}
#endif
		FOREACH(const shared_ptr<Engine>& e, OMEGA.getScene()->engines)
		{
			if (!e->label.empty()) {
				pyRunString("__builtins__." + e->label + "=Omega().labeledEngine('" + e->label + "')");
			}
#define _DO_FUNCTORS(functors, FunctorT)                                                                                                                       \
	{                                                                                                                                                      \
		FOREACH(const shared_ptr<FunctorT>& f, functors)                                                                                               \
		{                                                                                                                                              \
			if (!f->label.empty()) {                                                                                                               \
				pyRunString("__builtins__." + f->label + "=Omega().labeledEngine('" + f->label + "')");                                        \
			}                                                                                                                                      \
		}                                                                                                                                              \
	}
#define _TRY_DISPATCHER(DispatcherT)                                                                                                                           \
	{                                                                                                                                                      \
		DispatcherT* d = dynamic_cast<DispatcherT*>(e.get());                                                                                          \
		if (d) {                                                                                                                                       \
			_DO_FUNCTORS(d->functors, DispatcherT::FunctorType);                                                                                   \
		}                                                                                                                                              \
	}
			_TRY_DISPATCHER(BoundDispatcher);
			_TRY_DISPATCHER(IGeomDispatcher);
			_TRY_DISPATCHER(IPhysDispatcher);
			_TRY_DISPATCHER(LawDispatcher);
			InteractionLoop* id = dynamic_cast<InteractionLoop*>(e.get());
			if (id) {
				_DO_FUNCTORS(id->geomDispatcher->functors, IGeomFunctor);
				_DO_FUNCTORS(id->physDispatcher->functors, IPhysFunctor);
				_DO_FUNCTORS(id->lawDispatcher->functors, LawFunctor);
			}
			Collider* coll = dynamic_cast<Collider*>(e.get());
			if (coll) {
				_DO_FUNCTORS(coll->boundDispatcher->functors, BoundFunctor);
			}
#undef _DO_FUNCTORS
#undef _TRY_DISPATCHER
			CombinedKinematicEngine* cke = dynamic_cast<CombinedKinematicEngine*>(e.get());
			if (cke) {
				FOREACH(const shared_ptr<KinematicEngine>& ke, cke->comb)
				{
					if (!ke->label.empty()) {
						pyRunString("__builtins__." + ke->label + "=Omega().labeledEngine('" + ke->label + "')");
					}
				}
			}
		}
	}
	py::object labeled_engine_get(string label)
	{
		FOREACH(const shared_ptr<Engine>& e, OMEGA.getScene()->engines)
		{
#define _DO_FUNCTORS(functors, FunctorT)                                                                                                                       \
	{                                                                                                                                                      \
		FOREACH(const shared_ptr<FunctorT>& f, functors)                                                                                               \
		{                                                                                                                                              \
			if (f->label == label)                                                                                                                 \
				return py::object(f);                                                                                                          \
		}                                                                                                                                              \
	}
#define _TRY_DISPATCHER(DispatcherT)                                                                                                                           \
	{                                                                                                                                                      \
		DispatcherT* d = dynamic_cast<DispatcherT*>(e.get());                                                                                          \
		if (d) {                                                                                                                                       \
			_DO_FUNCTORS(d->functors, DispatcherT::FunctorType);                                                                                   \
		}                                                                                                                                              \
	}
			if (e->label == label) {
				return py::object(e);
			}
			_TRY_DISPATCHER(BoundDispatcher);
			_TRY_DISPATCHER(IGeomDispatcher);
			_TRY_DISPATCHER(IPhysDispatcher);
			_TRY_DISPATCHER(LawDispatcher);
			InteractionLoop* id = dynamic_cast<InteractionLoop*>(e.get());
			if (id) {
				_DO_FUNCTORS(id->geomDispatcher->functors, IGeomFunctor);
				_DO_FUNCTORS(id->physDispatcher->functors, IPhysFunctor);
				_DO_FUNCTORS(id->lawDispatcher->functors, LawFunctor);
			}
			Collider* coll = dynamic_cast<Collider*>(e.get());
			if (coll) {
				_DO_FUNCTORS(coll->boundDispatcher->functors, BoundFunctor);
			}
#undef _DO_FUNCTORS
#undef _TRY_DISPATCHER
			CombinedKinematicEngine* cke = dynamic_cast<CombinedKinematicEngine*>(e.get());
			if (cke) {
				FOREACH(const shared_ptr<KinematicEngine>& ke, cke->comb)
				{
					if (ke->label == label)
						return py::object(ke);
				}
			}
		}
		throw std::invalid_argument(string("No engine labeled `") + label + "'");
	}

	long iter() { return OMEGA.getScene()->iter; }
	int  subStep() { return OMEGA.getScene()->subStep; }
	bool subStepping_get() { return OMEGA.getScene()->subStepping; }
	void subStepping_set(bool val) { OMEGA.getScene()->subStepping = val; }

	Real time() { return OMEGA.getScene()->time; }
	Real realTime() { return OMEGA.getRealTime(); }
	Real speed() { return OMEGA.getScene()->speed; }
	Real dt_get() { return OMEGA.getScene()->dt; }
	void dt_set(Real dt)
	{
		Scene* scene = OMEGA.getScene().get();
		// activate timestepper, if possible (throw exception if there is none)
		if (dt < 0) {
			if (!scene->timeStepperActivate(true)) /* not activated*/
				throw runtime_error("No TimeStepper found in O.engines.");
		} else {
			scene->dt = dt;
		}
	}
	bool dynDt_get() { return OMEGA.getScene()->timeStepperActive(); }
	bool dynDt_set(bool activate)
	{
		if (not OMEGA.getScene()->timeStepperActivate(activate) and activate) /* not activated despite passed value */
			throw runtime_error("No TimeStepper found in O.engines.");
		return true;
	}
	bool dynDtAvailable_get() { return OMEGA.getScene()->timeStepperPresent(); }
	long stopAtIter_get() { return OMEGA.getScene()->stopAtIter; }
	void stopAtIter_set(long s) { OMEGA.getScene()->stopAtIter = s; }
	Real stopAtTime_get() { return OMEGA.getScene()->stopAtTime; }
	void stopAtTime_set(Real s) { OMEGA.getScene()->stopAtTime = s; }


	bool timingEnabled_get() { return TimingInfo::enabled; }
	void timingEnabled_set(bool enabled) { TimingInfo::enabled = enabled; }
	// deprecated:
	unsigned long forceSyncCount_get() { return OMEGA.getScene()->forces.syncCount; }
	void          forceSyncCount_set(unsigned long count) { OMEGA.getScene()->forces.syncCount = count; }

	void run(long int numIter = -1, bool doWait = false)
	{
		Scene* scene = OMEGA.getScene().get();
		if (numIter > 0)
			scene->stopAtIter = scene->iter + numIter;
		OMEGA.run();
		// timespec t1,t2; t1.tv_sec=0; t1.tv_nsec=40000000; /* 40 ms */
		// while(!OMEGA.isRunning()) nanosleep(&t1,&t2); // wait till we start, so that calling wait() immediately afterwards doesn't return immediately
		LOG_DEBUG(
		        "RUN" << ((scene->stopAtIter - scene->iter) > 0
		                          ? string(" (" + boost::lexical_cast<string>(scene->stopAtIter - scene->iter) + " to go)")
		                          : string(""))
		              << "!");
		if (doWait)
			wait();
	}
	void pause()
	{
		Py_BEGIN_ALLOW_THREADS;
		OMEGA.pause();
		Py_END_ALLOW_THREADS;
		LOG_DEBUG("PAUSE!");
	}
	void step()
	{
		if (OMEGA.isRunning())
			throw runtime_error("Called O.step() while simulation is running.");
		OMEGA.getScene()->moveToNextTimeStep(); /* LOG_DEBUG("STEP!"); run(1); wait(); */
	}
	void wait()
	{
		if (OMEGA.isRunning()) {
			LOG_DEBUG("WAIT!");
		} else
			return;
		timespec t1, t2;
		t1.tv_sec  = 0;
		t1.tv_nsec = 40000000; /* 40 ms */
		Py_BEGIN_ALLOW_THREADS;
		while (OMEGA.isRunning())
			nanosleep(&t1, &t2);
		Py_END_ALLOW_THREADS;
		if (!OMEGA.simulationLoop->workerThrew)
			return;
		LOG_ERROR("Simulation error encountered.");
		OMEGA.simulationLoop->workerThrew = false;
		throw OMEGA.simulationLoop->workerException;
	}
	bool       isRunning() { return OMEGA.isRunning(); }
	py::object get_filename()
	{
		string f = OMEGA.sceneFile;
		if (f.size() > 0)
			return py::object(f);
		return py::object();
	}
	void load(std::string fileName, bool quiet = false)
	{
		Py_BEGIN_ALLOW_THREADS;
		OMEGA.stop();
		Py_END_ALLOW_THREADS;
		OMEGA.loadSimulation(fileName, quiet);
		OMEGA.createSimulationLoop();
		mapLabeledEntitiesToVariables();
	}
	void     reload(bool quiet = false) { load(OMEGA.sceneFile, quiet); }
	void     saveTmp(string mark = "", bool quiet = false) { save(":memory:" + mark, quiet); }
	void     loadTmp(string mark = "", bool quiet = false) { load(":memory:" + mark, quiet); }
	py::list lsTmp()
	{
		py::list                          ret;
		typedef pair<std::string, string> strstr;
		FOREACH(const strstr& sim, OMEGA.memSavedSimulations)
		{
			string mark = sim.first;
			boost::algorithm::replace_first(mark, ":memory:", "");
			ret.append(mark);
		}
		return ret;
	}
	void tmpToFile(string mark, string filename)
	{
		if (OMEGA.memSavedSimulations.count(":memory:" + mark) == 0)
			throw runtime_error("No memory-saved simulation named " + mark);
		boost::iostreams::filtering_ostream out;
		if (boost::algorithm::ends_with(filename, ".bz2"))
			out.push(boost::iostreams::bzip2_compressor());
		out.push(boost::iostreams::file_sink(filename));
		if (!out.good())
			throw runtime_error("Error while opening file `" + filename + "' for writing.");
		LOG_INFO("Saving :memory:" << mark << " to " << filename);
		out << OMEGA.memSavedSimulations[":memory:" + mark];
	}
	string tmpToString(string mark)
	{
		if (OMEGA.memSavedSimulations.count(":memory:" + mark) == 0)
			throw runtime_error("No memory-saved simulation named " + mark);
		return OMEGA.memSavedSimulations[":memory:" + mark];
	}

	void reset()
	{
		OMEGA.stop();
		OMEGA.reset();
	}
	void resetThisScene()
	{
		Py_BEGIN_ALLOW_THREADS;
		OMEGA.stop();
		Py_END_ALLOW_THREADS;
		OMEGA.resetCurrentScene();
		OMEGA.createSimulationLoop();
	}
	void resetCurrentScene()
	{
		Py_BEGIN_ALLOW_THREADS;
		OMEGA.stop();
		Py_END_ALLOW_THREADS;
		OMEGA.resetCurrentScene();
		OMEGA.createSimulationLoop();
	}
	void resetTime()
	{
		OMEGA.getScene()->iter = 0;
		OMEGA.getScene()->time = 0;
		OMEGA.timeInit();
	}
	void switchScene() { std::swap(OMEGA.scenes[OMEGA.currentSceneNb], OMEGA.sceneAnother); }
	void resetAllScenes()
	{
		Py_BEGIN_ALLOW_THREADS;
		OMEGA.stop();
		Py_END_ALLOW_THREADS;
		OMEGA.resetAllScenes();
		OMEGA.createSimulationLoop();
	}
	void switchToScene(int i) { OMEGA.switchToScene(i); }
	int  addScene() { return OMEGA.addScene(); }

	// Scene manipulation in multithread situations as python object or as a string (e.g. FEMxDEM, MPI, ...)
	shared_ptr<Scene> scene_get() { return OMEGA.getScene(); }
	void              scene_set(const shared_ptr<Scene>& source)
	{
		Py_BEGIN_ALLOW_THREADS;
		reset();
		Py_END_ALLOW_THREADS;
		assertScene();
		OMEGA.setScene(source);
	}

#if PY_MAJOR_VERSION < 3
	string sceneToString() {
#else
	PyObject* sceneToString()
	{
#endif
		ostringstream oss;
	yade::ObjectIO::save<decltype(OMEGA.getScene()), boost::archive::binary_oarchive>(oss, "scene", OMEGA.getScene());
	oss.flush();
#if PY_MAJOR_VERSION < 3
	return oss.str();
#else
		const string s = oss.str();
		return PyBytes_FromStringAndSize(s.c_str(), s.length());
#endif
}

#ifdef YADE_MPI
//return vector<int> as contiguous bytes, skipping conversion to python list
PyObject*
intrsctToBytes(const shared_ptr<Subdomain>& subD, unsigned rank, bool mirror)
{
	if (subD->intersections.size() <= rank)
		LOG_ERROR("rank too large");
	if (not mirror)
		return PyBytes_FromStringAndSize((char*)&(subD->intersections[rank][0]), subD->intersections[rank].size() * sizeof(Body::id_t));
	else
		return PyBytes_FromStringAndSize((char*)&(subD->mirrorIntersections[rank][0]), subD->mirrorIntersections[rank].size() * sizeof(Body::id_t));
}
//return vector<int> as a writable contiguous array. Python syntax: bufferFromIntrsct(...)[:]=intrsctToBytes(...)
PyObject* bufferFromIntrsct(const shared_ptr<Subdomain>& subD, unsigned rank, unsigned size, bool mirror)
{
	//FIXME: if returning a memoryview, do we need to release it at some point? (https://docs.python.org/3/library/stdtypes.html#memoryview.release)
	if (subD->intersections.size() <= rank)
		LOG_ERROR("rank too large");
	if (not mirror) {
		if (subD->intersections[rank].size() != size)
			subD->intersections[rank].resize(size);
		return PyMemoryView_FromMemory((char*)(subD->intersections[rank].data()), subD->intersections[rank].size() * sizeof(Body::id_t), PyBUF_WRITE);
	} else {
		if (subD->mirrorIntersections[rank].size() != size)
			subD->mirrorIntersections[rank].resize(size);
		return PyMemoryView_FromMemory(
		        (char*)&(subD->mirrorIntersections[rank][0]), subD->mirrorIntersections[rank].size() * sizeof(Body::id_t), PyBUF_WRITE);
	}
}

#endif //YADE_MPI

void stringToScene(const string& sstring, string mark = "")
{
	Py_BEGIN_ALLOW_THREADS;
	OMEGA.stop();
	Py_END_ALLOW_THREADS;
	assertScene();
	OMEGA.memSavedSimulations[":memory:" + mark] = sstring;
	OMEGA.sceneFile                              = ":memory:" + mark;
	load(OMEGA.sceneFile, true);
}

int thisScene() { return OMEGA.currentSceneNb; }

void save(std::string fileName, bool quiet = false)
{
	assertScene();
	OMEGA.saveSimulation(fileName, quiet);
	// OMEGA.sceneFile=fileName; // done in Omega::saveSimulation;
}

py::list miscParams_get()
{
	py::list ret;
	FOREACH(shared_ptr<Serializable> & s, OMEGA.getScene()->miscParams) { ret.append(s); }
	return ret;
}

void miscParams_set(vector<shared_ptr<Serializable>> ss)
{
	vector<shared_ptr<Serializable>>& miscParams = OMEGA.getScene()->miscParams;
	miscParams.clear();
	FOREACH(shared_ptr<Serializable> s, ss) { miscParams.push_back(s); }
}


vector<shared_ptr<Engine>> engines_get(void)
{
	assertScene();
	Scene* scene = OMEGA.getScene().get();
	return scene->_nextEngines.empty() ? scene->engines : scene->_nextEngines;
}
void engines_set(const vector<shared_ptr<Engine>>& egs)
{
	assertScene();
	Scene* scene = OMEGA.getScene().get();
	if (scene->subStep < 0)
		scene->engines = egs; // not inside the engine loop right now, ok to update directly
	else
		scene->_nextEngines
		        = egs; // inside the engine loop, update _nextEngines; O.engines picks that up automatically, and Scene::moveToNextTimestep will put them in place of engines at the start of the next loop
	mapLabeledEntitiesToVariables();
}
// raw access to engines/_nextEngines, for debugging
vector<shared_ptr<Engine>> currEngines_get() { return OMEGA.getScene()->engines; }
vector<shared_ptr<Engine>> nextEngines_get() { return OMEGA.getScene()->_nextEngines; }

pyBodyContainer bodies_get(void)
{
	assertScene();
	return pyBodyContainer(OMEGA.getScene()->bodies);
}
pyInteractionContainer interactions_get(void)
{
	assertScene();
	return pyInteractionContainer(OMEGA.getScene()->interactions);
}

pyForceContainer    forces_get(void) { return pyForceContainer(OMEGA.getScene()); }
pyMaterialContainer materials_get(void) { return pyMaterialContainer(OMEGA.getScene()); }


py::list listChildClassesNonrecursive(const string& base)
{
	py::list ret;
	for (map<string, DynlibDescriptor>::const_iterator di = Omega::instance().getDynlibsDescriptor().begin();
	     di != Omega::instance().getDynlibsDescriptor().end();
	     ++di)
		if (Omega::instance().isInheritingFrom((*di).first, base))
			ret.append(di->first);
	return ret;
}

bool isChildClassOf(const string& child, const string& base) { return (Omega::instance().isInheritingFrom_recursive(child, base)); }

py::list plugins_get()
{
	const map<string, DynlibDescriptor>& plugins = Omega::instance().getDynlibsDescriptor();
	std::pair<string, DynlibDescriptor>  p;
	py::list                             ret;
	for (const auto& p : plugins)
		ret.append(p.first);
	return ret;
}

pyTags tags_get(void)
{
	assertScene();
	return pyTags(OMEGA.getScene());
}

void interactionContainer_set(string clss)
{
	Scene* rb = OMEGA.getScene().get();
	if (rb->interactions->size() > 0)
		throw std::runtime_error("Interaction container not empty, will not change its class.");
	shared_ptr<InteractionContainer> ic = YADE_PTR_DYN_CAST<InteractionContainer>(ClassFactory::instance().createShared(clss));
	rb->interactions                    = ic;
}
string interactionContainer_get(string /*clss*/) { return OMEGA.getScene()->interactions->getClassName(); }

void bodyContainer_set(string clss)
{
	Scene* rb = OMEGA.getScene().get();
	if (rb->bodies->size() > 0)
		throw std::runtime_error("Body container not empty, will not change its class.");
	shared_ptr<BodyContainer> bc = YADE_PTR_DYN_CAST<BodyContainer>(ClassFactory::instance().createShared(clss));
	rb->bodies                   = bc;
}
string bodyContainer_get(string /*clss*/) { return OMEGA.getScene()->bodies->getClassName(); }
#ifdef YADE_OPENMP
int  numThreads_get() { return omp_get_max_threads(); }
void numThreads_set(int n)
{
	int bcn = OMEGA.getScene()->forces.getNumAllocatedThreads();
	if (bcn < n)
		LOG_WARN(
		        "ForceContainer has only " << bcn << " threads allocated. Changing thread number to on " << bcn << " instead of " << n
		                                   << " requested.");
	omp_set_num_threads(min(n, bcn));
	LOG_WARN("BUG: Omega().numThreads=n doesn't work as expected (number of threads is not changed globally). Set env var OMP_NUM_THREADS instead.");
}
#else
	int  numThreads_get() { return 1; }
	void numThreads_set(int) { LOG_WARN("Yade was compiled without openMP support, changing number of threads will have no effect."); }
#endif

shared_ptr<Cell> cell_get()
{
	if (OMEGA.getScene()->isPeriodic)
		return OMEGA.getScene()->cell;
	return shared_ptr<Cell>();
}
bool periodic_get(void) { return OMEGA.getScene()->isPeriodic; }
void periodic_set(bool v) { OMEGA.getScene()->isPeriodic = v; }

shared_ptr<EnergyTracker> energy_get() { return OMEGA.getScene()->energy; }
bool                      trackEnergy_get(void) { return OMEGA.getScene()->trackEnergy; }
void                      trackEnergy_set(bool e) { OMEGA.getScene()->trackEnergy = e; }

void disableGdb()
{
	signal(SIGSEGV, SIG_DFL);
	signal(SIGABRT, SIG_DFL);
}
void exitNoBacktrace(int status = 0)
{
	if (status == 0)
		signal(SIGSEGV, termHandlerNormal); /* unset the handler that runs gdb and prints backtrace */
	else
		signal(SIGSEGV, termHandlerError);
	// try to clean our mess
	Omega::instance().cleanupTemps();
	// flush all streams (so that in case we crash at exit, unflushed buffers are not lost)
	fflush(NULL);
	// attempt exit
	exit(status);
}
void runEngine(const shared_ptr<Engine>& e)
{
	LOG_WARN("Omega().runEngine(): deprecated, use __call__ method of the engine instance directly instead; will be removed in the future.");
	e->scene = OMEGA.getScene().get();
	e->action();
}
std::string tmpFilename() { return OMEGA.tmpFilename(); }
};

class pyGenericPotential : public GenericPotential, public py::wrapper<GenericPotential> {
public:
	Real potential(Real const& u, LubricationPhys const& phys) const
	{
		TRACE;
		return contactForce(u, phys.a) + potentialForce(u, phys.a);
	}

	void applyPotential(Real const& u, LubricationPhys& phys, Vector3r const& n)
	{
		TRACE;
		phys.normalContactForce   = contactForce(u, phys.a) * n;
		phys.normalPotentialForce = potentialForce(u, phys.a) * n;
		phys.contact              = hasContact(u, phys.a);
	}

	virtual Real contactForce(Real const& u, Real const& a) const
	{
		TRACE;
		gilLock lock;
		LOG_TRACE("GIL State: " << PyGILState_Check());
		return get_override("contactForce")(u, a);
	}

	virtual Real potentialForce(Real const& u, Real const& a) const
	{
		TRACE;
		gilLock lock;
		return get_override("potentialForce")(u, a);
	}

	virtual bool hasContact(Real const& u, Real const& a) const
	{
		TRACE;
		gilLock lock;
		return get_override("hasContact")(u, a);
	}
};

} // namespace yade


// BOOST_PYTHON_MODULE cannot be inside yade namespace, it has 'extern "C"' keyword, which strips it out of any namespaces.
BOOST_PYTHON_MODULE(wrapper)
try {
	using namespace yade; // 'using namespace' inside function keeps namespace pollution under control. Alernatively I could add y:: in front of function names below and put 'namespace y  = ::yade;' here.
	namespace py                = ::boost::python;
	py::scope().attr("__doc__") = "Wrapper for c++ internals of yade.";

	YADE_SET_DOCSTRING_OPTS;

	// keep in sync with lib/serialization/Serializable.hpp !
	py::enum_<yade::Attr::flags>("AttrFlags")
	        .value("noSave", yade::Attr::noSave)
	        .value("readonly", yade::Attr::readonly)
	        .value("triggerPostLoad", yade::Attr::triggerPostLoad)
	        .value("noResize", yade::Attr::noResize);

	py::class_<pyOmega>("Omega")
	        .add_property("iter", &pyOmega::iter, "Get current step number")
	        .add_property(
	                "subStep",
	                &pyOmega::subStep,
	                "Get the current subStep number (only meaningful if O.subStepping==True); -1 when outside the loop, otherwise either 0 "
	                "(O.subStepping==False) or number of engine to be run (O.subStepping==True)")
	        .add_property("subStepping", &pyOmega::subStepping_get, &pyOmega::subStepping_set, "Get/set whether subStepping is active.")
	        .add_property(
	                "stopAtIter", &pyOmega::stopAtIter_get, &pyOmega::stopAtIter_set, "Get/set number of iteration after which the simulation will stop.")
	        .add_property("stopAtTime", &pyOmega::stopAtTime_get, &pyOmega::stopAtTime_set, "Get/set time after which the simulation will stop.")
	        .add_property("time", &pyOmega::time, "Return virtual (model world) time of the simulation.")
	        .add_property("realtime", &pyOmega::realTime, "Return clock (human world) time the simulation has been running.")
	        .add_property("speed", &pyOmega::speed, "Return current calculation speed [iter/sec].")
	        .add_property("dt", &pyOmega::dt_get, &pyOmega::dt_set, "Current timestep (Δt) value.")
	        .add_property(
	                "dynDt",
	                &pyOmega::dynDt_get,
	                &pyOmega::dynDt_set,
	                "Whether a :yref:`TimeStepper` is used for dynamic Δt control. See :yref:`dt<Omega.dt>` on how to enable/disable :yref:`TimeStepper`.")
	        .add_property(
	                "dynDtAvailable",
	                &pyOmega::dynDtAvailable_get,
	                "Whether a :yref:`TimeStepper` is amongst :yref:`O.engines<Omega.engines>`, activated or not.")
	        .def("load",
	             &pyOmega::load,
	             (py::arg("file"), py::arg("quiet") = false),
	             "Load simulation from file. The file should be :yref:`saved<Omega.save>` in the same version of Yade, otherwise compatibility is not "
	             "guaranteed.")
	        .def("reload", &pyOmega::reload, (py::arg("quiet") = false), "Reload current simulation")
	        .def("save",
	             &pyOmega::save,
	             (py::arg("file"), py::arg("quiet") = false),
	             "Save current simulation to file (should be .xml or .xml.bz2 or .yade or .yade.gz). .xml files are bigger than .yade, but can be more or "
	             "less easily (due to their size) opened and edited, e.g. with text editors. .bz2 and .gz correspond both to compressed versions. All "
	             "saved files should be :yref:`loaded<Omega.load>` in the same version of Yade, otherwise compatibility is not guaranteed.")
	        .def("loadTmp",
	             &pyOmega::loadTmp,
	             (py::arg("mark") = "", py::arg("quiet") = false),
	             "Load simulation previously stored in memory by saveTmp. *mark* optionally distinguishes multiple saved simulations")
	        .def("saveTmp",
	             &pyOmega::saveTmp,
	             (py::arg("mark") = "", py::arg("quiet") = false),
	             "Save simulation to memory (disappears at shutdown), can be loaded later with loadTmp. *mark* optionally distinguishes different "
	             "memory-saved simulations.")
	        .def("lsTmp", &pyOmega::lsTmp, "Return list of all memory-saved simulations.")
	        .def("tmpToFile",
	             &pyOmega::tmpToFile,
	             (py::arg("fileName"), py::arg("mark") = ""),
	             "Save XML of :yref:`saveTmp<Omega.saveTmp>`'d simulation into *fileName*.")
	        .def("tmpToString", &pyOmega::tmpToString, (py::arg("mark") = ""), "Return XML of :yref:`saveTmp<Omega.saveTmp>`'d simulation as string.")
	        .def("run",
	             &pyOmega::run,
	             (py::arg("nSteps") = -1, py::arg("wait") = false),
	             "Run the simulation. *nSteps* how many steps to run, then stop (if positive); *wait* will cause not returning to python until simulation "
	             "will have stopped.")
	        .def("pause", &pyOmega::pause, "Stop simulation execution. (May be called from within the loop, and it will stop after the current step).")
	        .def("step", &pyOmega::step, "Advance the simulation by one step. Returns after the step will have finished.")
	        .def("wait", &pyOmega::wait, "Don't return until the simulation will have been paused. (Returns immediately if not running).")
	        .add_property("running", &pyOmega::isRunning, "Whether background thread is currently running a simulation.")
	        .add_property("filename", &pyOmega::get_filename, "Filename under which the current simulation was saved (None if never saved).")
	        .def("reset", &pyOmega::reset, "Reset simulations completely (including another scenes!).")
	        .def("resetThisScene", &pyOmega::resetThisScene, "Reset current scene.")
	        .def("resetCurrentScene", &pyOmega::resetCurrentScene, "Reset current scene.")
	        .def("resetAllScenes", &pyOmega::resetAllScenes, "Reset all scenes.")
	        .def("addScene", &pyOmega::addScene, "Add new scene to Omega, returns its number")
	        .def("switchToScene",
	             &pyOmega::switchToScene,
	             "Switch to defined scene. Default scene has number 0, other scenes have to be created by addScene method.")
	        .def("switchScene",
	             &pyOmega::switchScene,
	             "Switch to alternative simulation (while keeping the old one). Calling the function again switches back to the first one. Note that most "
	             "variables from the first simulation will still refer to the first simulation even after the switch\n(e.g. b=O.bodies[4]; "
	             "O.switchScene(); [b still refers to the body in the first simulation here])")
	        .add_property("thisScene", &pyOmega::thisScene, "Return current scene's id.")
	        .def("sceneToString",
	             &pyOmega::sceneToString,
	             "Return the entire scene as a string. Equivalent to using O.save(...) except that the scene goes to a string instead of a file. (see also "
	             "stringToScene())")
	        .def("stringToScene",
	             &pyOmega::stringToScene,
	             (py::arg("mark") = ""),
	             "Load simulation from a string passed as argument (see also sceneToString).")
	        .def("labeledEngine",
	             &pyOmega::labeled_engine_get,
	             // FIXME: use R"""(raw text)""" here, like exaplained in https://yade-dem.org/doc/prog.html#sphinx-documentation and used in py/_libVersions.cpp
	             "Return instance of engine/functor with the given label. This function shouldn't be called by the user directly; every ehange in "
	             "O.engines will assign respective global python variables according to labels.\n\nFor example:\n\n\t "
	             "*O.engines=[InsertionSortCollider(label='collider')]*\n\n\t *collider.nBins=5 # collider has become a variable after assignment to "
	             "O.engines automatically*")
	        .def("resetTime",
	             &pyOmega::resetTime,
	             "Reset simulation time: step number, virtual and real time. (Doesn't touch anything else, including timings).")
	        .def("plugins", &pyOmega::plugins_get, "Return list of all plugins registered in the class factory.")
	        // 		.def("_sceneObj",&pyOmega::scene_get,"Return the :yref:`scene <Scene>` object. Debugging only, all (or most) :yref:`Scene` functionality is proxies through :yref:`Omega`.")
	        .add_property(
	                "_sceneObj",
	                &pyOmega::scene_get,
	                &pyOmega::scene_set,
	                "Return the :yref:`scene <Scene>` object. Debugging only, all (or most) :yref:`Scene` functionality is proxies through :yref:`Omega`.")
	        .add_property(
	                "engines",
	                &pyOmega::engines_get,
	                &pyOmega::engines_set,
	                "List of engines in the simulation (corresponds to Scene::engines in C++ source code).")
	        .add_property("_currEngines", &pyOmega::currEngines_get, "Currently running engines; debugging only!")
	        .add_property(
	                "_nextEngines",
	                &pyOmega::nextEngines_get,
	                "Engines for the next step, if different from the current ones, otherwise empty; debugging only!")
	        .add_property(
	                "miscParams",
	                &pyOmega::miscParams_get,
	                &pyOmega::miscParams_set,
	                "MiscParams in the simulation (Scene::mistParams), usually used to save serializables that don't fit anywhere else, like GL functors")
	        .add_property("bodies", &pyOmega::bodies_get, "Bodies in the current simulation (container supporting index access by id and iteration)")
	        .add_property(
	                "interactions",
	                &pyOmega::interactions_get,
	                "Access to :yref:`interactions<Interaction>` of simulation, by using \n\n#. id's of both :yref:`Bodies<Body>` of the interactions, "
	                "e.g. ``O.interactions[23,65]``\n#. iteraction over the whole container::\n\n\tfor i in O.interactions: print i.id1,i.id2\n\n.. "
	                "note::\n\tIteration silently skips interactions that are not :yref:`real<Interaction.isReal>`.")
	        .add_property("materials", &pyOmega::materials_get, "Shared materials; they can be accessed by id or by label")
	        .add_property("forces", &pyOmega::forces_get, ":yref:`ForceContainer` (forces, torques, displacements) in the current simulation.")
	        .add_property(
	                "energy",
	                &pyOmega::energy_get,
	                ":yref:`EnergyTracker` of the current simulation. (meaningful only with :yref:`O.trackEnergy<Omega.trackEnergy>`)")
	        .add_property(
	                "trackEnergy", &pyOmega::trackEnergy_get, &pyOmega::trackEnergy_set, "When energy tracking is enabled or disabled in this simulation.")
	        .add_property(
	                "tags",
	                &pyOmega::tags_get,
	                "Tags (string=string dictionary) of the current simulation (container supporting string-index access/assignment)")
	        .def("childClassesNonrecursive",
	             &pyOmega::listChildClassesNonrecursive,
	             "Return list of all classes deriving from given class, as registered in the class factory")
	        .def("isChildClassOf", &pyOmega::isChildClassOf, "Tells whether the first class derives from the second one (both given as strings).")
	        .add_property(
	                "timingEnabled",
	                &pyOmega::timingEnabled_get,
	                &pyOmega::timingEnabled_set,
	                "Globally enable/disable timing services (see documentation of the :yref:`timing module<yade.timing>`).")
	        .add_property(
	                "forceSyncCount",
	                &pyOmega::forceSyncCount_get,
	                &pyOmega::forceSyncCount_set,
	                "Counter for number of syncs in ForceContainer, for profiling purposes.")
	        .add_property("numThreads", &pyOmega::numThreads_get /* ,&pyOmega::numThreads_set*/, "Get maximum number of threads openMP can use.")
	        .add_property("cell", &pyOmega::cell_get, "Periodic cell of the current scene (None if the scene is aperiodic).")
	        .add_property("periodic", &pyOmega::periodic_get, &pyOmega::periodic_set, "Get/set whether the scene is periodic or not (True/False).")
	        .def("exitNoBacktrace",
	             &pyOmega::exitNoBacktrace,
	             (py::arg("status") = 0),
	             "Disable SEGV handler and exit, optionally with given status number.")
	        .def("disableGdb", &pyOmega::disableGdb, "Revert SEGV and ABRT handlers to system defaults.")
	        .def("runEngine",
	             &pyOmega::runEngine,
	             "Run given engine exactly once; simulation time, step number etc. will not be incremented (use only if you know what you do).")
	        .def("tmpFilename", &pyOmega::tmpFilename, "Return unique name of file in temporary directory which will be deleted when yade exits.")
#ifdef YADE_MPI
	        .def("intrsctToBytes",
	             &pyOmega::intrsctToBytes,
	             (py::arg("subdomain"), py::arg("rank"), py::arg("mirror")),
	             "returns a copy of intersections[rank] (a vector<int>) from a subdomain in the form of bytes. Returns a copy mirrorIntersections[rank] if "
	             "mirror=True.")
	        .def("bufferFromIntrsct",
	             &pyOmega::bufferFromIntrsct,
	             (py::arg("subdomain"), py::arg("rank"), py::arg("size"), py::arg("mirror")),
	             "returns a (char*) pointer to the underying buffer of intersections[rank], so that it can be overwritten. Size must be passed in advance. "
	             "Pointer to mirrorIntersections[rank] is returned if mirror=True. Python syntax: bufferFromIntrsct(...)[:]=bytes(something)")
#endif
	        ;
	py::class_<pyTags>(
	        "TagsWrapper",
	        "Container emulating dictionary semantics for accessing tags associated with simulation. Tags are accesed by strings.",
	        py::init<pyTags&>())
	        .def("__getitem__", &pyTags::getItem)
	        .def("__setitem__", &pyTags::setItem)
	        .def("keys", &pyTags::keys)
	        .def("has_key", &pyTags::hasKey);
	py::class_<pyBodyContainer>("BodyContainer", py::init<pyBodyContainer&>())
	        .def("__getitem__", &pyBodyContainer::pyGetitem)
	        .def("__len__", &pyBodyContainer::length)
	        .def("__iter__", &pyBodyContainer::pyIter)
	        .def("append", &pyBodyContainer::append, "Append one Body instance, return its id.")
	        .def("append", &pyBodyContainer::appendList, "Append list of Body instance, return list of ids")
	        .def("appendClumped",
	             &pyBodyContainer::appendClump,
	             (py::arg("discretization") = 0),
	             "Append given list of bodies as a clump (rigid aggregate); returns a tuple of ``(clumpId,[memberId1,memberId2,...])``. Clump masses and "
	             "inertia are adapted automatically (for details see :yref:`clump()<BodyContainer.clump>`).")
	        .def("clump",
	             &pyBodyContainer::clump,
	             (py::arg("discretization") = 0),
	             "Clump given bodies together (creating a rigid aggregate); returns ``clumpId``. Clump masses and inertia are adapted automatically when "
	             "discretization>0. If clump members are overlapping this is done by integration/summation over mass points using a regular grid of cells "
	             "(grid cells length is defined as $R_{min}/discretization$, where $R_{min}$ is minimum clump member radius). For non-overlapping members "
	             "inertia of the clump is the sum of inertias from members. If discretization<=0 sum of inertias from members is used (faster, but "
	             "inaccurate).")
	        .def("updateClumpProperties",
	             &pyBodyContainer::updateClumpProperties,
	             (py::arg("excludeList") = py::list(), py::arg("discretization") = 5),
	             "Manually force Yade to update clump properties mass, volume and inertia (for details of 'discretization' value see "
	             ":yref:`clump()<BodyContainer.clump>`). Can be used, when clumps are modified or erased during a simulation. Clumps can be excluded from "
	             "the calculation by giving a list of ids: *O.bodies.updateProperties([ids])*.")
	        .def("deleteClumpMember", &pyBodyContainer::deleteClumpMember, "Erase clump member.") //FIXME
	        .def("deleteClumpBody", &pyBodyContainer::deleteClumpBody, "Erase clump member.")     //FIXME
	        .def("addToClump",
	             &pyBodyContainer::addToClump,
	             (py::arg("discretization") = 0),
	             "Add body b (or a list of bodies) to an existing clump c. c must be clump and b may not be a clump member of c. Clump masses and inertia "
	             "are adapted automatically (for details see :yref:`clump()<BodyContainer.clump>`).\n\nSee :ysrc:`examples/clumps/addToClump-example.py` "
	             "for an example script.\n\n.. note:: If b is a clump itself, then all members will be added to c and b will be deleted. If b is a clump "
	             "member of clump d, then all members from d will be added to c and d will be deleted. If you need to add just clump member b, "
	             ":yref:`release<BodyContainer.releaseFromClump>` this member from d first.")
	        .def("releaseFromClump",
	             &pyBodyContainer::releaseFromClump,
	             (py::arg("discretization") = 0),
	             "Release body b from clump c. b must be a clump member of c. Clump masses and inertia are adapted automatically (for details see "
	             ":yref:`clump()<BodyContainer.clump>`).\n\nSee :ysrc:`examples/clumps/releaseFromClump-example.py` for an example script.\n\n.. note:: If "
	             "c contains only 2 members b will not be released and a warning will appear. In this case clump c should be "
	             ":yref:`erased<BodyContainer.erase>`.")
	        .def("replaceByClumps",
	             &pyBodyContainer::replaceByClumps,
	             (py::arg("discretization") = 0),
	             "Replace spheres by clumps using a list of clump templates and a list of amounts; returns a list of tuples: "
	             "``[(clumpId1,[memberId1,memberId2,...]),(clumpId2,[memberId1,memberId2,...]),...]``. A new clump will have the same volume as the "
	             "sphere, that was replaced. Clump masses and inertia are adapted automatically (for details see :yref:`clump()<BodyContainer.clump>`). "
	             "\n\n\t *O.bodies.replaceByClumps( [utils.clumpTemplate([1,1],[.5,.5])] , [.9] ) #will replace 90 % of all standalone spheres by "
	             "'dyads'*\n\nSee :ysrc:`examples/clumps/replaceByClumps-example.py` for an example script.")
	        .def("getRoundness",
	             &pyBodyContainer::getRoundness,
	             (py::arg("excludeList") = py::list()),
	             "Returns roundness coefficient RC = R2/R1. R1 is the equivalent sphere radius of a clump. R2 is the minimum radius of a sphere, that "
	             "imbeds the clump. If just spheres are present RC = 1. If clumps are present 0 < RC < 1. Bodies can be excluded from the calculation by "
	             "giving a list of ids: *O.bodies.getRoundness([ids])*.\n\nSee :ysrc:`examples/clumps/replaceByClumps-example.py` for an example script.")
	        .def("clear", &pyBodyContainer::clear, "Remove all bodies (interactions not checked)")
	        .def("erase",
	             &pyBodyContainer::erase,
	             (py::arg("eraseClumpMembers") = 0),
	             "Erase body with the given id; all interaction will be deleted by InteractionLoop in the next step. If a clump is erased use "
	             "*O.bodies.erase(clumpId,True)* to erase the clump AND its members.")
	        .def("replace", &pyBodyContainer::replace)
	        .def("insertAtId", &pyBodyContainer::insertAtId, (py::arg("insertatid")), "Insert a body at theid, (no body should exist in this id)")
#ifdef YADE_MPI
	        .def("subdomainBodies", &pyBodyContainer::subdomainBodies, "id's of bodies with bounds in MPI subdomain")
#endif //YADE_MPI
	        .add_property(
	                "useRedirection",
	                &pyBodyContainer::getUseRedirection,
	                &pyBodyContainer::setUseRedirection,
	                "true if the scene uses up-to-date lists for boundedBodies and realBodies; turned true automatically 1/ after removal of bodies if "
	                ":yref:`enableRedirection`=True, and 2/ in MPI execution.")
	        .add_property(
	                "enableRedirection",
	                &pyBodyContainer::getEnableRedirection,
	                &pyBodyContainer::setEnableRedirection,
	                "let collider switch to optimized algorithm with body redirection when bodies are erased - true by default");
	py::class_<pyBodyIterator>("BodyIterator", py::init<pyBodyIterator&>())
	        .def("__iter__", &pyBodyIterator::pyIter)
	        .def("__next__", &pyBodyIterator::pyNext);
	py::class_<pyInteractionContainer>(
	        "InteractionContainer",
	        "Access to :yref:`interactions<Interaction>` of simulation, by using \n\n#. id's of both :yref:`Bodies<Body>` of the interactions, e.g. "
	        "``O.interactions[23,65]``\n#. iteraction over the whole container::\n\n\tfor i in O.interactions: print i.id1,i.id2\n\n.. note::\n\tIteration "
	        "silently skips interactions that are not :yref:`real<Interaction.isReal>`.",
	        py::init<pyInteractionContainer&>())
	        .def("__iter__", &pyInteractionContainer::pyIter)
	        .def("__getitem__", &pyInteractionContainer::pyGetitem)
	        .def("__len__", &pyInteractionContainer::len)
	        .def("has", &pyInteractionContainer::has, "Tell if a pair of ids corresponds to an existing interaction (real or not)")
	        .def("countReal", &pyInteractionContainer::countReal, "Return number of interactions that are \"real\", i.e. they have phys and geom.")
	        .def("nth",
	             &pyInteractionContainer::pyNth,
	             "Return n-th interaction from the container (usable for picking random interaction). The virtual interactions are not reached.")
	        .def("withBody", &pyInteractionContainer::withBody, "Return list of real interactions of given body.")
	        .def("withBodyAll", &pyInteractionContainer::withBodyAll, "Return list of all (real as well as non-real) interactions of given body.")
	        .def("all",
	             &pyInteractionContainer::getAll,
	             (py::arg("onlyReal") = false),
	             "Return list of all interactions. Virtual interaction are filtered out if onlyReal=True, else (default) it dumps the full content.")
	        .def("eraseNonReal", &pyInteractionContainer::eraseNonReal, "Erase all interactions that are not :yref:`real <Interaction.isReal>`.")
	        .def("erase",
	             &pyInteractionContainer::erase,
	             "Erase one interaction, given by id1, id2 (internally, ``requestErase`` is called -- the interaction might still exist as potential, if "
	             "the :yref:`Collider` decides so).")
	        .add_property("serializeSorted", &pyInteractionContainer::serializeSorted_get, &pyInteractionContainer::serializeSorted_set)
	        .def("clear",
	             &pyInteractionContainer::clear,
	             "Remove all interactions, and invalidate persistent collider data (if the collider supports it).");
	py::class_<pyInteractionIterator>("InteractionIterator", py::init<pyInteractionIterator&>())
	        .def("__iter__", &pyInteractionIterator::pyIter)
	        .def("__next__", &pyInteractionIterator::pyNext);

	py::class_<pyForceContainer>("ForceContainer", py::init<pyForceContainer&>())
	        .def("f",
	             &pyForceContainer::force_get,
	             (py::arg("id"), py::arg("sync") = false),
	             "Force applied on body. For clumps in openMP, synchronize the force container with sync=True, else the value will be wrong.")
	        .def("t",
	             &pyForceContainer::torque_get,
	             (py::arg("id"), py::arg("sync") = false),
	             "Torque applied on body. For clumps in openMP, synchronize the force container with sync=True, else the value will be wrong.")
	        .def("m", &pyForceContainer::torque_get, (py::arg("id"), py::arg("sync") = false), "Deprecated alias for t (torque).")
	        .def("addF",
	             &pyForceContainer::force_add,
	             (py::arg("id"), py::arg("f"), py::arg("permanent") = false),
	             "Apply force on body (accumulates). The force applies for one iteration, then it is reset by ForceResetter. \n # permanent parameter is "
	             "deprecated, instead of addF(...,permanent=True) use setPermF(...).")
	        .def("addT",
	             &pyForceContainer::torque_add,
	             (py::arg("id"), py::arg("t"), py::arg("permanent") = false),
	             "Apply torque on body (accumulates). The torque applies for one iteration, then it is reset by ForceResetter. \n # permanent parameter is "
	             "deprecated, instead of addT(...,permanent=True) use setPermT(...).")
	        .def("permF", &pyForceContainer::permForce_get, (py::arg("id")), "read the value of permanent force on body (set with setPermF()).")
	        .def("permT", &pyForceContainer::permTorque_get, (py::arg("id")), "read the value of permanent torque on body (set with setPermT()).")
	        .def("setPermF", &pyForceContainer::permForce_set, "set the value of permanent force on body.")
	        .def("setPermT", &pyForceContainer::permTorque_set, "set the value of permanent torque on body.")
	        .def("reset",
	             &pyForceContainer::reset,
	             (py::arg("resetAll") = true),
	             "Reset the force container, including user defined permanent forces/torques. resetAll=False will keep permanent forces/torques unchanged.")
	        .def("getPermForceUsed", &pyForceContainer::getPermForceUsed, "Check wether permanent forces are present.")
	        .add_property(
	                "syncCount",
	                &pyForceContainer::syncCount_get,
	                &pyForceContainer::syncCount_set,
	                "Number of synchronizations  of ForceContainer (cummulative); if significantly higher than number of steps, there might be unnecessary "
	                "syncs hurting performance.");

	py::class_<pyMaterialContainer>(
	        "MaterialContainer",
	        "Container for :yref:`Materials<Material>`. A material can be accessed using \n\n #. numerical index in range(0,len(cont)), like cont[2]; \n "
	        "#. textual label that was given to the material, like cont['steel']. This etails traversing all materials and should not be used frequently.",
	        py::init<pyMaterialContainer&>())
	        .def("append", &pyMaterialContainer::append, "Add new shared :yref:`Material`; changes its id and return it.")
	        .def("append", &pyMaterialContainer::appendList, "Append list of :yref:`Material` instances, return list of ids.")
	        .def("index", &pyMaterialContainer::index, "Return id of material, given its label.")
	        .def("__getitem__", &pyMaterialContainer::getitem_id)
	        .def("__getitem__", &pyMaterialContainer::getitem_label)
	        .def("__len__", &pyMaterialContainer::len);

	py::class_<STLImporter>("STLImporter").def("ymport", &STLImporter::import);

	py::class_<pyGenericPotential, boost::noncopyable>("GenericPotential")
	        .def("contactForce", py::pure_virtual(&pyGenericPotential::contactForce), "This function should return contact force norm.")
	        .def("potentialForce", py::pure_virtual(&pyGenericPotential::potentialForce), "This function should return potential force norm.")
	        .def("hasContact", py::pure_virtual(&pyGenericPotential::hasContact), "This function should return true if there are contact.");

	//////////////////////////////////////////////////////////////
	///////////// proxyless wrappers
	Serializable().pyRegisterClass(py::scope());

	py::class_<TimingDeltas, shared_ptr<TimingDeltas>, boost::noncopyable>("TimingDeltas")
	        .add_property("data", &TimingDeltas::pyData, "Get timing data as list of tuples (label, execTime[nsec], execCount) (one tuple per checkpoint)")
	        .def("reset", &TimingDeltas::reset, "Reset timing information");

	py::scope().attr("O") = pyOmega();

} catch (...) {
	LOG_FATAL("Importing this module caused an exception and this module is in an inconsistent state now.");
	PyErr_Print();
	PyErr_SetString(PyExc_SystemError, __FILE__);
	boost::python::handle_exception();
	throw;
}

