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aka_array_tmpl.hh
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			/**
			* @file aka_array_tmpl.hh
			*
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Thu Jul 15 2010
			* @date last modification: Tue Sep 02 2014
			*
			* @brief Inline functions of the classes Array<T> and ArrayBase
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
			* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
			*
			* Akantu is free software: you can redistribute it and/or modify it under the
			* terms of the GNU Lesser General Public License as published by the Free
			* Software Foundation, either version 3 of the License, or (at your option) any
			* later version.
			*
			* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
			* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
			* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
			* details.
			*
			* You should have received a copy of the GNU Lesser General Public License
			* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
			*
			*/

			/* -------------------------------------------------------------------------- */
			/* Inline Functions Array<T> */
			/* -------------------------------------------------------------------------- */

			__END_AKANTU__

			#include <memory>

			__BEGIN_AKANTU__

			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			inline T & Array<T, is_scal>::operator()(UInt i, UInt j) {
			AKANTU_DEBUG_ASSERT(size > 0,
			"The array \"" << id << "\" is empty");
			AKANTU_DEBUG_ASSERT((i < size) && (j < nb_component),
			"The value at position [" << i << "," << j
			<< "] is out of range in array \"" << id << "\"");
			return values[i*nb_component + j];
			}

			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			inline const T & Array<T, is_scal>::operator()(UInt i, UInt j) const {
			AKANTU_DEBUG_ASSERT(size > 0,
			"The array \"" << id << "\" is empty");
			AKANTU_DEBUG_ASSERT((i < size) && (j < nb_component),
			"The value at position [" << i << "," << j
			<< "] is out of range in array \"" << id << "\"");
			return values[i*nb_component + j];
			}

			template <class T, bool is_scal>
			inline T & Array<T, is_scal>::operator[](UInt i) {
			AKANTU_DEBUG_ASSERT(size > 0,
			"The array \"" << id << "\" is empty");
			AKANTU_DEBUG_ASSERT((i < size*nb_component),
			"The value at position [" << i << "] is out of range in array \"" << id << "\"");
			return values[i];
			}

			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			inline const T & Array<T, is_scal>::operator[](UInt i) const {
			AKANTU_DEBUG_ASSERT(size > 0,
			"The array \"" << id << "\" is empty");
			AKANTU_DEBUG_ASSERT((i < size*nb_component),
			"The value at position [" << i << "] is out of range in array \"" << id << "\"");
			return values[i];
			}



			/* -------------------------------------------------------------------------- */
			/**
			* append a tuple to the array with the value value for all components
			* @param value the new last tuple or the array will contain nb_component copies of value
			*/
			template <class T, bool is_scal>
			inline void Array<T, is_scal>::push_back(const T & value) {
			UInt pos = size;

			resizeUnitialized(size+1);

			std::uninitialized_fill_n(values + pos * nb_component, nb_component, value);
			}

			/* -------------------------------------------------------------------------- */
			/**
			* append a tuple to the array
			* @param new_elem a C-array containing the values to be copied to the end of the array */
			template <class T, bool is_scal>
			inline void Array<T, is_scal>::push_back(const T new_elem[]) {
			UInt pos = size;

			resizeUnitialized(size+1);

			T * tmp = values + nb_component * pos;
			std::uninitialized_copy(new_elem, new_elem + nb_component, tmp);
			}

			/* -------------------------------------------------------------------------- */
			/**
			* append a matrix or a vector to the array
			* @param new_elem a reference to a Matrix<T> or Vector<T> */
			template <class T, bool is_scal>
			template<template<typename> class C>
			inline void Array<T, is_scal>::push_back(const C<T> & new_elem) {
			AKANTU_DEBUG_ASSERT(nb_component == new_elem.size(),
			"The vector("<< new_elem.size() <<") as not a size compatible with the Array (nb_component=" << nb_component << ").");
			UInt pos = size;
			resizeUnitialized(size+1);

			T * tmp = values + nb_component * pos;
			std::uninitialized_copy(new_elem.storage(), new_elem.storage() + nb_component, tmp);
			}

			/* -------------------------------------------------------------------------- */
			/**
			* append a tuple to the array
			* @param it an iterator to the tuple to be copied to the end of the array */
			template <class T, bool is_scal>
			template<class Ret>
			inline void Array<T, is_scal>::push_back(const Array<T, is_scal>::iterator<Ret> & it) {
			UInt pos = size;

			resizeUnitialized(size+1);

			T * tmp = values + nb_component * pos;
			T * new_elem = it.data();
			std::uninitialized_copy(new_elem, new_elem + nb_component, tmp);
			}

			/* -------------------------------------------------------------------------- */
			/**
			* erase an element. If the erased element is not the last of the array, the
			* last element is moved into the hole in order to maintain contiguity. This
			* may invalidate existing iterators (For instance an iterator obtained by
			* Array::end() is no longer correct) and will change the order of the
			* elements.
			* @param i index of element to erase
			*/
			template <class T, bool is_scal>
			inline void Array<T, is_scal>::erase(UInt i){
			AKANTU_DEBUG_IN();
			AKANTU_DEBUG_ASSERT((size > 0),
			"The array is empty");
			AKANTU_DEBUG_ASSERT((i < size),
			"The element at position [" << i << "] is out of range (" << i << ">=" << size << ")");


			if(i != (size - 1)) {
			for (UInt j = 0; j < nb_component; ++j) {
			values[inb_component + j] = values[(size-1)nb_component + j];
			}
			}

			resize(size - 1);
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Subtract another array entry by entry from this array in place. Both arrays must
			* have the same size and nb_component. If the arrays have different shapes,
			* code compiled in debug mode will throw an expeption and optimised code
			* will behave in an unpredicted manner
			* @param other array to subtract from this
			* @return reference to modified this
			*/
			template <class T, bool is_scal>
			Array<T, is_scal> & Array<T, is_scal>::operator-=(const Array<T, is_scal> & vect) {
			AKANTU_DEBUG_ASSERT((size == vect.size) && (nb_component == vect.nb_component),
			"The too array don't have the same sizes");

			T * a = values;
			T * b = vect.storage();
			for (UInt i = 0; i < size*nb_component; ++i) {
			a -= b;
			++a;++b;
			}

			return *this;
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Add another array entry by entry to this array in place. Both arrays must
			* have the same size and nb_component. If the arrays have different shapes,
			* code compiled in debug mode will throw an expeption and optimised code
			* will behave in an unpredicted manner
			* @param other array to add to this
			* @return reference to modified this
			*/
			template <class T, bool is_scal>
			Array<T, is_scal> & Array<T, is_scal>::operator+=(const Array<T, is_scal> & vect) {
			AKANTU_DEBUG_ASSERT((size == vect.size) && (nb_component == vect.nb_component),
			"The too array don't have the same sizes");

			T * a = values;
			T * b = vect.storage();
			for (UInt i = 0; i < size*nb_component; ++i) {
			a++ += b++;
			}

			return *this;
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Multiply all entries of this array by a scalar in place
			* @param alpha scalar multiplicant
			* @return reference to modified this
			*/
			template <class T, bool is_scal>
			Array<T, is_scal> & Array<T, is_scal>::operator*=(const T & alpha) {
			T * a = values;
			for (UInt i = 0; i < size*nb_component; ++i) {
			a++ = alpha;
			}

			return *this;
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Compare this array element by element to another.
			* @param other array to compare to
			* @return true it all element are equal and arrays have the same shape, else false
			*/
			template <class T, bool is_scal>
			bool Array<T, is_scal>::operator==(const Array<T, is_scal> & array) const {
			bool equal = nb_component == array.nb_component && size == array.size && id == array.id;
			if(!equal) return false;

			if(values == array.storage()) return true;
			else return std::equal(values, values + size*nb_component,
			array.storage());
			}

			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			bool Array<T, is_scal>::operator!=(const Array<T, is_scal> & array) const {
			return !operator==(array);
			}

			/* -------------------------------------------------------------------------- */
			/**
			* set all tuples of the array to a given vector or matrix
			* @param vm Matrix or Vector to fill the array with
			*/
			template <class T, bool is_scal>
			template<template<typename> class C>
			inline void Array<T, is_scal>::set(const C<T> & vm) {
			AKANTU_DEBUG_ASSERT(nb_component == vm.size(),
			"The size of the object does not match the number of components");
			for (T * it = values;
			it < values + nb_component * size;
			it += nb_component) {
			std::copy(vm.storage(), vm.storage() + nb_component, it);
			}
			}

			/* -------------------------------------------------------------------------- */
			/* Functions Array<T, is_scal> */
			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			Array<T, is_scal>::Array (UInt size,
			UInt nb_component,
			const ID & id) :
			ArrayBase(id), values(NULL) {
			AKANTU_DEBUG_IN();
			allocate(size, nb_component);

			if(!is_scal) {
			T val = T();
			std::uninitialized_fill(values, values + size*nb_component, val);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			Array<T, is_scal>::Array (UInt size,
			UInt nb_component,
			const T def_values[],
			const ID & id) :
			ArrayBase(id), values(NULL) {
			AKANTU_DEBUG_IN();
			allocate(size, nb_component);

			T * tmp = values;

			for (UInt i = 0; i < size; ++i) {
			tmp = values + nb_component * i;
			std::uninitialized_copy(def_values, def_values + nb_component, tmp);
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			Array<T, is_scal>::Array (UInt size,
			UInt nb_component,
			const T & value,
			const ID & id) :
			ArrayBase(id), values(NULL) {
			AKANTU_DEBUG_IN();
			allocate(size, nb_component);

			std::uninitialized_fill_n(values, size*nb_component, value);

			AKANTU_DEBUG_OUT();
			}


			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			Array<T, is_scal>::Array(const Array<T, is_scal> & vect,
			bool deep,
			const ID & id) {
			AKANTU_DEBUG_IN();
			this->id = (id == "") ? vect.id : id;

			if (deep) {
			allocate(vect.size, vect.nb_component);
			T * tmp = values;
			std::uninitialized_copy(vect.storage(), vect.storage() + size * nb_component, tmp);
			} else {
			this->values = vect.storage();
			this->size = vect.size;
			this->nb_component = vect.nb_component;
			this->allocated_size = vect.allocated_size;
			this->size_of_type = vect.size_of_type;
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			#ifndef SWIG
			template <class T, bool is_scal>
			Array<T, is_scal>::Array(const std::vector<T>& vect) {
			AKANTU_DEBUG_IN();
			this->id = "";

			allocate(vect.size(), 1);
			T * tmp = values;
			std::uninitialized_copy(&(vect[0]), &(vect[size-1]), tmp);

			AKANTU_DEBUG_OUT();
			}
			#endif

			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			Array<T, is_scal>::~Array () {
			AKANTU_DEBUG_IN();
			AKANTU_DEBUG(dblAccessory, "Freeing "
			<< printMemorySize<T>(allocated_size*nb_component)
			<< " (" << id <<")");

			if(values){
			if(!is_scal)
			for (UInt i = 0; i < size * nb_component; ++i) {
			T * obj = values+i;
			obj->~T();
			}
			free(values);
			}
			size = allocated_size = 0;
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			/**
			* perform the allocation for the constructors
			* @param size is the size of the array
			* @param nb_component is the number of component of the array
			*/
			template <class T, bool is_scal>
			void Array<T, is_scal>::allocate(UInt size,
			UInt nb_component) {
			AKANTU_DEBUG_IN();
			if (size == 0){
			values = NULL;
			} else {
			values = static_cast<T>(malloc(nb_component size * sizeof(T)));
			AKANTU_DEBUG_ASSERT(values != NULL,
			"Cannot allocate "
			<< printMemorySize<T>(size*nb_component)
			<< " (" << id <<")");
			}

			if (values == NULL) {
			this->size = this->allocated_size = 0;
			} else {
			AKANTU_DEBUG(dblAccessory, "Allocated "
			<< printMemorySize<T>(size*nb_component)
			<< " (" << id <<")");
			this->size = this->allocated_size = size;
			}

			this->size_of_type = sizeof(T);
			this->nb_component = nb_component;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			/**
			* change the size of the array and allocate or free memory if needed. If the
			* size increases, the new tuples are filled with zeros
			* @param new_size new number of tuples contained in the array */
			template <class T, bool is_scal>
			void Array<T, is_scal>::resize(UInt new_size) {
			UInt old_size = size;

			T * old_values = values;
			if(new_size < size) {
			for (UInt i = new_size * nb_component; i < size * nb_component; ++i) {
			T * obj = old_values+i;
			obj->~T();
			}
			}

			resizeUnitialized(new_size);


			T val = T();
			if(size > old_size)
			std::uninitialized_fill(values + old_sizenb_component, values + sizenb_component, val);
			}

			/* -------------------------------------------------------------------------- */
			/**
			* change the size of the array and allocate or free memory if needed.
			* @param new_size new number of tuples contained in the array */
			template <class T, bool is_scal>
			void Array<T, is_scal>::resizeUnitialized(UInt new_size) {
			// AKANTU_DEBUG_IN();
			// free some memory
			if(new_size <= allocated_size) {
			if(allocated_size - new_size > AKANTU_MIN_ALLOCATION) {
			AKANTU_DEBUG(dblAccessory, "Freeing "
			<< printMemorySize<T>((allocated_size - size)*nb_component)
			<< " (" << id <<")");

			// Normally there are no allocation problem when reducing an array
			T * tmp_ptr = static_cast<T>(realloc(values, new_size nb_component * sizeof(T)));
			if(new_size != 0 && tmp_ptr == NULL) {
			AKANTU_DEBUG_ERROR("Cannot free data (" << id << ")"
			<< " [current allocated size : " << allocated_size << " \| "
			<< "requested size : " << new_size << "]");
			}
			values = tmp_ptr;
			allocated_size = new_size;
			}

			size = new_size;

			// AKANTU_DEBUG_OUT();
			return;
			}

			// allocate more memory
			UInt size_to_alloc = (new_size - allocated_size < AKANTU_MIN_ALLOCATION) ?
			allocated_size + AKANTU_MIN_ALLOCATION : new_size;

			T tmp_ptr = static_cast<T>(realloc(values, size_to_alloc * nb_component * sizeof(T)));
			AKANTU_DEBUG_ASSERT(tmp_ptr != NULL,
			"Cannot allocate "
			<< printMemorySize<T>(size_to_alloc * nb_component));
			if (tmp_ptr == NULL) {
			AKANTU_DEBUG_ERROR("Cannot allocate more data (" << id << ")"
			<< " [current allocated size : " << allocated_size << " \| "
			<< "requested size : " << new_size << "]");
			}

			AKANTU_DEBUG(dblAccessory, "Allocating "
			<< printMemorySize<T>((size_to_alloc - allocated_size)*nb_component));

			allocated_size = size_to_alloc;
			size = new_size;
			values = tmp_ptr;

			// AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			/**
			* change the number of components by interlacing data
			* @param multiplicator number of interlaced components add
			* @param block_size blocks of data in the array
			* Examaple for block_size = 2, multiplicator = 2
			* array = oo oo oo -> new array = oo nn nn oo nn nn oo nn nn */
			template <class T, bool is_scal>
			void Array<T, is_scal>::extendComponentsInterlaced(UInt multiplicator,
			UInt block_size) {
			AKANTU_DEBUG_IN();

			if (multiplicator == 1) return;

			AKANTU_DEBUG_ASSERT(multiplicator > 1,
			"invalid multiplicator");
			AKANTU_DEBUG_ASSERT(nb_component%block_size == 0,
			"stride must divide actual number of components");

			values = static_cast<T>(realloc(values, nb_componentmultiplicatorsize sizeof(T)));

			UInt new_component = nb_component/block_size * multiplicator;

			for (UInt i = 0,k=size-1; i < size; ++i,--k) {
			for (UInt j = 0; j < new_component; ++j) {
			UInt m = new_component - j -1;
			UInt n = m/multiplicator;
			for (UInt l = 0,p=block_size-1; l < block_size; ++l,--p) {
			values[knb_componentmultiplicator+m*block_size+p] =
			values[knb_component+nblock_size+p];
			}
			}
			}

			nb_component = nb_component * multiplicator;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			/**
			* search elem in the array, return the position of the first occurrence or
			* -1 if not found
			* @param elem the element to look for
			* @return index of the first occurrence of elem or -1 if elem is not present
			*/
			template <class T, bool is_scal>
			Int Array<T, is_scal>::find(const T & elem) const {
			AKANTU_DEBUG_IN();
			UInt i = 0;
			for (; (i < size) && (values[i] != elem); ++i);

			AKANTU_DEBUG_OUT();
			return (i == size) ? -1 : (Int) i;
			}

			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			Int Array<T, is_scal>::find(T elem[]) const {
			AKANTU_DEBUG_IN();
			T * it = values;
			UInt i = 0;
			for (;i < size; ++i) {
			if(*it == elem[0]) {
			T * cit = it;
			UInt c = 0;
			for(; (c < nb_component) && (*cit == elem[c]); ++c, ++cit);
			if(c == nb_component) {
			AKANTU_DEBUG_OUT();
			return i;
			}
			}
			it += nb_component;
			}
			return -1;
			}


			/* -------------------------------------------------------------------------- */
			/**
			* copy the content of another array. This overwrites the current content.
			* @param other Array to copy into this array. It has to have the same
			* nb_component as this. If compiled in debug mode, an incorrect other will
			* result in an exception being thrown. Optimised code may result in
			* unpredicted behaviour.
			*/
			template <class T, bool is_scal>
			void Array<T, is_scal>::copy(const Array<T, is_scal>& vect, bool no_sanity_check) {
			AKANTU_DEBUG_IN();

			if(!no_sanity_check)
			if(vect.nb_component != nb_component)
			AKANTU_DEBUG_ERROR("The two arrays do not have the same number of components");

			resize((vect.size * vect.nb_component) / nb_component);

			T * tmp = values;
			std::uninitialized_copy(vect.storage(), vect.storage() + size * nb_component, tmp);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			template<bool is_scal>
			class ArrayPrintHelper {
			public:
			template<typename T>
			static void print_content(const Array<T> & vect, std::ostream & stream, int indent) {
			if(AKANTU_DEBUG_TEST(dblDump) \|\| AKANTU_DEBUG_LEVEL_IS_TEST()) {
			std::string space;
			for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);

			stream << space << " + values : {";
			for (UInt i = 0; i < vect.getSize(); ++i) {
			stream << "{";
			for (UInt j = 0; j < vect.getNbComponent(); ++j) {
			stream << vect(i, j);
			if(j != vect.getNbComponent() - 1) stream << ", ";
			}
			stream << "}";
			if(i != vect.getSize() - 1) stream << ", ";
			}
			stream << "}" << std::endl;
			}
			}
			};

			template<>
			class ArrayPrintHelper<false> {
			public:
			template<typename T>
			static void print_content(__attribute__((unused)) const Array<T> & vect,
			__attribute__((unused)) std::ostream & stream,
			__attribute__((unused)) int indent) { }
			};


			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			void Array<T, is_scal>::printself(std::ostream & stream, int indent) const {
			std::string space;
			for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);

			std::streamsize prec = stream.precision();
			std::ios_base::fmtflags ff = stream.flags();

			stream.setf (std::ios_base::showbase);
			stream.precision(2);

			stream << space << "Array<" << debug::demangle(typeid(T).name()) << "> [" << std::endl;
			stream << space << " + id : " << this->id << std::endl;
			stream << space << " + size : " << this->size << std::endl;
			stream << space << " + nb_component : " << this->nb_component << std::endl;
			stream << space << " + allocated size : " << this->allocated_size << std::endl;
			stream << space << " + memory size : "
			<< printMemorySize<T>(allocated_size*nb_component) << std::endl;
			if(!AKANTU_DEBUG_LEVEL_IS_TEST())
			stream << space << " + address : " << std::hex << this->values
			<< std::dec << std::endl;

			stream.precision(prec);
			stream.flags(ff);

			ArrayPrintHelper<is_scal>::print_content(*this, stream, indent);

			stream << space << "]" << std::endl;
			}

			/* -------------------------------------------------------------------------- */
			/* Inline Functions ArrayBase */
			/* -------------------------------------------------------------------------- */

			inline UInt ArrayBase::getMemorySize() const {
			return allocated_size * nb_component * size_of_type;
			}

			inline void ArrayBase::empty() {
			size = 0;
			}

			/* -------------------------------------------------------------------------- */
			/* Iterators */
			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			template<class R, class IR, bool is_r_scal>
			class Array<T, is_scal>::iterator_internal {
			public:
			typedef R value_type;
			typedef R* pointer;
			typedef R& reference;
			typedef typename R::proxy proxy;
			typedef const typename R::proxy const_proxy;
			typedef const R& const_reference;
			typedef IR internal_value_type;
			typedef IR* internal_pointer;
			typedef std::ptrdiff_t difference_type;
			typedef std::random_access_iterator_tag iterator_category;

			public:
			iterator_internal() : _offset(0), initial(NULL), ret(NULL), ret_ptr(NULL) {};

			iterator_internal(pointer_type data, UInt _offset) :
			_offset(_offset),
			initial(data),
			ret(NULL),
			ret_ptr(data) {
			AKANTU_DEBUG_ERROR("The constructor should never be called it is just an ugly trick...");
			}

			iterator_internal(pointer wrapped) : _offset(wrapped->size()),
			initial(wrapped->storage()),
			ret(const_cast<internal_pointer>(wrapped)),
			ret_ptr(wrapped->storage()) {
			}

			iterator_internal(const iterator_internal & it) {
			if(this != &it) {
			this->_offset = it._offset;
			this->initial = it.initial;
			this->ret_ptr = it.ret_ptr;
			this->ret = new internal_value_type(*it.ret, false);
			}
			}

			virtual ~iterator_internal() { delete ret; };

			inline iterator_internal & operator=(const iterator_internal & it) {
			if(this != &it) {
			this->_offset = it._offset;
			this->initial = it.initial;
			this->ret_ptr = it.ret_ptr;
			if(this->ret) this->ret->shallowCopy(*it.ret);
			else this->ret = new internal_value_type(*it.ret, false);
			}
			return *this;
			}

			UInt getCurrentIndex(){return (this->ret_ptr - this->initial)/this->_offset;};

			inline reference operator() { ret->values = ret_ptr; return ret; };
			inline const_reference operator() const { ret->values = ret_ptr; return ret; };
			inline pointer operator->() { ret->values = ret_ptr; return ret; };
			inline iterator_internal & operator++() { ret_ptr += _offset; return *this; };
			inline iterator_internal & operator--() { ret_ptr -= _offset; return *this; };

			inline iterator_internal & operator+=(const UInt n) { ret_ptr += _offset * n; return *this; }
			inline iterator_internal & operator-=(const UInt n) { ret_ptr -= _offset * n; return *this; }

			inline proxy operator[](const UInt n) { ret->values = ret_ptr + n_offset; return proxy(ret); }
			inline const_proxy operator[](const UInt n) const { ret->values = ret_ptr + n_offset; return const_proxy(ret); }

			inline bool operator==(const iterator_internal & other) const { return this->ret_ptr == other.ret_ptr; }
			inline bool operator!=(const iterator_internal & other) const { return this->ret_ptr != other.ret_ptr; }
			inline bool operator <(const iterator_internal & other) const { return this->ret_ptr < other.ret_ptr; }
			inline bool operator<=(const iterator_internal & other) const { return this->ret_ptr <= other.ret_ptr; }
			inline bool operator> (const iterator_internal & other) const { return this->ret_ptr > other.ret_ptr; }
			inline bool operator>=(const iterator_internal & other) const { return this->ret_ptr >= other.ret_ptr; }

			inline iterator_internal operator+(difference_type n) { iterator_internal tmp(*this); tmp += n; return tmp; }
			inline iterator_internal operator-(difference_type n) { iterator_internal tmp(*this); tmp -= n; return tmp; }


			inline difference_type operator-(const iterator_internal & b) { return (this->ret_ptr - b.ret_ptr) / _offset; }


			inline pointer_type data() const { return ret_ptr; }
			inline difference_type offset() const { return _offset; }

			protected:
			UInt _offset;
			pointer_type initial;
			internal_pointer ret;
			pointer_type ret_ptr;
			};

			/* -------------------------------------------------------------------------- */
			/**
			* Specialization for scalar types
			*/
			template <class T, bool is_scal>
			template <class R, class IR>
			class Array<T, is_scal>::iterator_internal<R, IR, true> {
			public:
			typedef R value_type;
			typedef R* pointer;
			typedef R& reference;
			typedef const R& const_reference;
			typedef IR internal_value_type;
			typedef IR* internal_pointer;
			typedef std::ptrdiff_t difference_type;
			typedef std::random_access_iterator_tag iterator_category;

			public:
			iterator_internal(pointer data = NULL, __attribute__ ((unused)) UInt _offset = 1) : _offset(_offset), ret(data), initial(data) { };
			iterator_internal(const iterator_internal & it) {
			if(this != &it) { this->ret = it.ret; this->initial = it.initial; }
			}

			virtual ~iterator_internal() { };

			inline iterator_internal & operator=(const iterator_internal & it)
			{ if(this != &it) { this->ret = it.ret; this->initial = it.initial; } return *this; }

			UInt getCurrentIndex(){return (this->ret - this->initial)/this->_offset;};

			inline reference operator() { return ret; };
			inline const_reference operator() const { return ret; };
			inline pointer operator->() { return ret; };
			inline iterator_internal & operator++() { ++ret; return *this; };
			inline iterator_internal & operator--() { --ret; return *this; };

			inline iterator_internal & operator+=(const UInt n) { ret += n; return *this; }
			inline iterator_internal & operator-=(const UInt n) { ret -= n; return *this; }

			inline reference operator[](const UInt n) { return ret[n]; }

			inline bool operator==(const iterator_internal & other) const { return ret == other.ret; }
			inline bool operator!=(const iterator_internal & other) const { return ret != other.ret; }
			inline bool operator< (const iterator_internal & other) const { return ret < other.ret; }
			inline bool operator<=(const iterator_internal & other) const { return ret <= other.ret; }
			inline bool operator> (const iterator_internal & other) const { return ret > other.ret; }
			inline bool operator>=(const iterator_internal & other) const { return ret >= other.ret; }

			inline iterator_internal operator-(difference_type n) { return iterator_internal(ret - n); }
			inline iterator_internal operator+(difference_type n) { return iterator_internal(ret + n); }

			inline difference_type operator-(const iterator_internal & b) { return ret - b.ret; }

			inline pointer data() const { return ret; }
			inline difference_type offset() const { return _offset; }
			protected:
			difference_type _offset;
			pointer ret;
			pointer initial;
			};

			/* -------------------------------------------------------------------------- */
			/* Begin/End functions implementation */
			/* -------------------------------------------------------------------------- */
			/* -------------------------------------------------------------------------- */
			/**
			* Get an iterator that behaves like a pointer akantu::Vector<T> * to the
			* first tuple of the array.
			* @param n vector size. Has to be equal to nb_component. This unfortunate
			* redundancy is necessary to distinguish it from ::begin() which it
			* overloads. If compiled in debug mode, an incorrect value of n will result
			* in an exception being thrown. Optimized code will fail in an unpredicted
			* manner.
			* @return a vector_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::vector_iterator Array<T, is_scal>::begin(UInt n) {
			AKANTU_DEBUG_ASSERT(nb_component == n,
			"The iterator is not compatible with the type Array("
			<< n<< ")");
			return vector_iterator(new Vector<T>(values, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get an iterator that behaves like a pointer akantu::Vector<T> * pointing
			* past the last tuple of the array.
			* @param n vector size. see Array::begin(UInt n) for more
			* @return a vector_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::vector_iterator Array<T, is_scal>::end(UInt n) {
			AKANTU_DEBUG_ASSERT(nb_component == n,
			"The iterator is not compatible with the type Array("
			<< n<< ")");
			return vector_iterator(new Vector<T>(values + nb_component * size,
			n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get a const iterator that behaves like a pointer akantu::Vector<T> * to the
			* first tuple of the array.
			* @param n vector size. see Array::begin(UInt n) for more
			* @return a vector_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::const_vector_iterator Array<T, is_scal>::begin(UInt n) const {
			AKANTU_DEBUG_ASSERT(nb_component == n,
			"The iterator is not compatible with the type Array("
			<< n<< ")");
			return const_vector_iterator(new Vector<T>(values, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get a const iterator that behaves like a pointer akantu::Vector<T> * pointing
			* past the last tuple of the array.
			* @param n vector size. see Array::begin(UInt n) for more
			* @return a const_vector_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::const_vector_iterator Array<T, is_scal>::end(UInt n) const {
			AKANTU_DEBUG_ASSERT(nb_component == n,
			"The iterator is not compatible with the type Array("
			<< n<< ")");
			return const_vector_iterator(new Vector<T>(values + nb_component * size,
			n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get an iterator that behaves like a pointer akantu::Vector<T> * to the
			* first tuple of the array.
			*
			* The reinterpret iterators allow to iterate over an array in any way that
			* preserves the number of entries of the array. This can for instance be use
			* full if the shape of the data in an array is not initially known.
			* @param n vector size.
			* @param size number of tuples in array. n times size must match the number
			* of entries of the array. If compiled in debug mode, an incorrect
			* combination of n and size will result
			* in an exception being thrown. Optimized code will fail in an unpredicted
			* manner.
			* @return a vector_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::vector_iterator
			Array<T, is_scal>::begin_reinterpret(UInt n, __attribute__((unused)) UInt size) {
			AKANTU_DEBUG_ASSERT(n * size == this->nb_component * this->size,
			"The new values for size (" << size
			<< ") and nb_component (" << n
			<< ") are not compatible with the one of this array("
			<< this->size << "," << this->nb_component << ")");
			return vector_iterator(new Vector<T>(values, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get an iterator that behaves like a pointer akantu::Vector<T> * pointing
			* past the last tuple of the array.
			* @param n vector size.
			* @param size number of tuples in array. See Array::begin_reinterpret(UInt n, UInt size)
			* @return a vector_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::vector_iterator
			Array<T, is_scal>::end_reinterpret(UInt n, UInt size) {
			AKANTU_DEBUG_ASSERT(n * size == this->nb_component * this->size,
			"The new values for size (" << size
			<< ") and nb_component (" << n
			<< ") are not compatible with the one of this array("
			<< this->size << "," << this->nb_component << ")");
			return vector_iterator(new Vector<T>(values + n * size, n));
			}


			/* -------------------------------------------------------------------------- */
			/**
			* Get a const iterator that behaves like a pointer akantu::Vector<T> * to the
			* first tuple of the array.
			* @param n vector size.
			* @param size number of tuples in array. See Array::begin_reinterpret(UInt n, UInt size)
			* @return a const_vector_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::const_vector_iterator
			Array<T, is_scal>::begin_reinterpret(UInt n, __attribute__((unused)) UInt size) const {
			AKANTU_DEBUG_ASSERT(n * size == this->nb_component * this->size,
			"The new values for size (" << size
			<< ") and nb_component (" << n
			<< ") are not compatible with the one of this array("
			<< this->size << "," << this->nb_component << ")");
			return const_vector_iterator(new Vector<T>(values, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get a const iterator that behaves like a pointer akantu::Vector<T> * pointing
			* past the last tuple of the array.
			* @param n vector size.
			* @param size number of tuples in array. See Array::begin_reinterpret(UInt n, UInt size)
			* @return a const_vector_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::const_vector_iterator
			Array<T, is_scal>::end_reinterpret(UInt n, UInt size) const {
			AKANTU_DEBUG_ASSERT(n * size == this->nb_component * this->size,
			"The new values for size (" << size
			<< ") and nb_component (" << n
			<< ") are not compatible with the one of this array("
			<< this->size << "," << this->nb_component << ")");
			return const_vector_iterator(new Vector<T>(values + n * size, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get an iterator that behaves like a pointer akantu::Matrix<T> * to the
			* first tuple of the array.
			* @param m number of rows
			* @param n number of columns. m times n has to equal nb_component.
			* If compiled in debug mode, an incorrect combination of m and n will result
			* in an exception being thrown. Optimized code will fail in an unpredicted
			* manner.
			* @return a matrix_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::matrix_iterator Array<T, is_scal>::begin(UInt m, UInt n) {
			AKANTU_DEBUG_ASSERT(nb_component == n*m,
			"The iterator is not compatible with the type Matrix("
			<< m << "," << n<< ")");
			return matrix_iterator(new Matrix<T>(values, m, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get an iterator that behaves like a pointer akantu::Matrix<T> * pointing
			* past the last tuple of the array.
			* @param m number of rows
			* @param n number of columns. See Array::begin(UInt m, UInt n)
			* @return a matrix_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::matrix_iterator Array<T, is_scal>::end(UInt m, UInt n) {
			AKANTU_DEBUG_ASSERT(nb_component == n*m,
			"The iterator is not compatible with the type Matrix("
			<< m << "," << n<< ")");
			return matrix_iterator(new Matrix<T>(values + nb_component * size, m, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get a const iterator that behaves like a pointer akantu::Matrix<T> * to the
			* first tuple of the array.
			* @param m number of rows
			* @param n number of columns. See Array::begin(UInt m, UInt n)
			* @return a matrix_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::const_matrix_iterator Array<T, is_scal>::begin(UInt m, UInt n) const {
			AKANTU_DEBUG_ASSERT(nb_component == n*m,
			"The iterator is not compatible with the type Matrix("
			<< m << "," << n<< ")");
			return const_matrix_iterator(new Matrix<T>(values, m, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get a const iterator that behaves like a pointer akantu::Matrix<T> * pointing
			* past the last tuple of the array.
			* @param m number of rows
			* @param n number of columns. See Array::begin(UInt m, UInt n)
			* @return a const_matrix_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::const_matrix_iterator Array<T, is_scal>::end(UInt m, UInt n) const {
			AKANTU_DEBUG_ASSERT(nb_component == n*m,
			"The iterator is not compatible with the type Matrix("
			<< m << "," << n<< ")");
			return const_matrix_iterator(new Matrix<T>(values + nb_component * size, m, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get an iterator that behaves like a pointer akantu::Matrix<T> * to the
			* first tuple of the array.
			*
			* The reinterpret iterators allow to iterate over an array in any way that
			* preserves the number of entries of the array. This can for instance be use
			* full if the shape of the data in an array is not initially known.
			* @param m number of rows
			* @param n number of columns
			* @param size number of tuples in array. m times n times size must match the number
			* of entries of the array. If compiled in debug mode, an incorrect
			* combination of m, n and size will result
			* in an exception being thrown. Optimized code will fail in an unpredicted
			* manner.
			* @return a matrix_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::matrix_iterator
			Array<T, is_scal>::begin_reinterpret(UInt m, UInt n, __attribute__((unused)) UInt size) {
			AKANTU_DEBUG_ASSERT(n * m * size == this->nb_component * this->size,
			"The new values for size (" << size
			<< ") and nb_component (" << m << "," << n << " = " << n * m
			<< ") are not compatible with the one of this array("
			<< this->size << "," << this->nb_component << ")");
			return matrix_iterator(new Matrix<T>(values, m, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get an iterator that behaves like a pointer akantu::Matrix<T> * pointing
			* past the last tuple of the array.
			* @param m number of rows
			* @param n number of columns
			* @param size number of tuples in array. See Array::begin_reinterpret(UInt m, UInt n, UInt size)
			* @return a matrix_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::matrix_iterator
			Array<T, is_scal>::end_reinterpret(UInt m, UInt n, UInt size) {
			AKANTU_DEBUG_ASSERT(n * m * size == this->nb_component * this->size,
			"The new values for size (" << size
			<< ") and nb_component (" << m << "," << n << " = " << n * m
			<< ") are not compatible with the one of this array("
			<< this->size << "," << this->nb_component << ")");
			return matrix_iterator(new Matrix<T>(values + n * m * size, m, n));
			}


			/* -------------------------------------------------------------------------- */
			/**
			* Get a const iterator that behaves like a pointer akantu::Matrix<T> * to the
			* first tuple of the array.
			* @param m number of rows
			* @param n number of columns
			* @param size number of tuples in array. See Array::begin_reinterpret(UInt m, UInt n, UInt size)
			* @return a const_matrix_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::const_matrix_iterator
			Array<T, is_scal>::begin_reinterpret(UInt m, UInt n, __attribute__((unused)) UInt size) const {
			AKANTU_DEBUG_ASSERT(n * m * size == this->nb_component * this->size,
			"The new values for size (" << size
			<< ") and nb_component (" << m << "," << n << " = " << n * m
			<< ") are not compatible with the one of this array("
			<< this->size << "," << this->nb_component << ")");
			return const_matrix_iterator(new Matrix<T>(values, m, n));
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Get a const iterator that behaves like a pointer akantu::Matrix<T> * pointing
			* past the last tuple of the array.
			* @param m number of rows
			* @param n number of columns
			* @param size number of tuples in array. See Array::begin_reinterpret(UInt m, UInt n, UInt size)
			* @return a const_matrix_iterator
			*/
			template <class T, bool is_scal>
			inline typename Array<T, is_scal>::const_matrix_iterator
			Array<T, is_scal>::end_reinterpret(UInt m, UInt n, UInt size) const {
			AKANTU_DEBUG_ASSERT(n * m * size == this->nb_component * this->size,
			"The new values for size (" << size
			<< ") and nb_component (" << m << "," << n << " = " << n * m
			<< ") are not compatible with the one of this array("
			<< this->size << "," << this->nb_component << ")");
			return const_matrix_iterator(new Matrix<T>(values + n * m * size, m, n));
			}

			/* -------------------------------------------------------------------------- */
			/** Get an iterator that behaves like a pointer T * to the
			* first entry in the member array values
			* @return a scalar_iterator
			*/
			template <class T, bool is_scal>
			inline Array<T, is_scal>::iterator<T> Array<T, is_scal>::begin() {
			AKANTU_DEBUG_ASSERT(nb_component == 1, "this iterator cannot be used on a vector which has nb_component != 1");
			return iterator<T>(values);
			}

			/* -------------------------------------------------------------------------- */
			/! Get an iterator that behaves like a pointer T that points past the
			* last entry in the member array values
			* @return a scalar_iterator
			*/
			template <class T, bool is_scal>
			inline Array<T, is_scal>::iterator<T> Array<T, is_scal>::end() {
			AKANTU_DEBUG_ASSERT(nb_component == 1, "this iterator cannot be used on a array which has nb_component != 1");
			return iterator<T>(values + size);
			}

			/* -------------------------------------------------------------------------- */
			/! Get a const iterator that behaves like a pointer T to the
			* first entry in the member array values
			* @return a const_scalar_iterator
			*/
			template <class T, bool is_scal>
			inline Array<T, is_scal>::const_iterator<T> Array<T, is_scal>::begin() const {
			AKANTU_DEBUG_ASSERT(nb_component == 1, "this iterator cannot be used on a array which has nb_component != 1");
			return const_iterator<T>(values);
			}

			/* -------------------------------------------------------------------------- */
			/! Get a const iterator that behaves like a pointer T that points past the
			* last entry in the member array values
			* @return a const_scalar_iterator
			*/
			template <class T, bool is_scal>
			inline Array<T, is_scal>::const_iterator<T> Array<T, is_scal>::end() const {
			AKANTU_DEBUG_ASSERT(nb_component == 1, "this iterator cannot be used on a array which has nb_component != 1");
			return const_iterator<T>(values + size);
			}

			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			template<typename R>
			class Array<T, is_scal>::const_iterator : public iterator_internal<const R, R> {
			public:
			typedef iterator_internal<const R, R> parent;
			typedef typename parent::value_type value_type;
			typedef typename parent::pointer pointer;
			typedef typename parent::reference reference;
			typedef typename parent::difference_type difference_type;
			typedef typename parent::iterator_category iterator_category;
			public:

			const_iterator() : parent() {};
			const_iterator(pointer_type data, UInt offset) : parent(data, offset) {}
			const_iterator(pointer warped) : parent(warped) {}
			const_iterator(const parent & it) : parent(it) {}
			// const_iterator(const const_iterator<R> & it) : parent(it) {}

			inline const_iterator operator+(difference_type n)
			{ return parent::operator+(n); }
			inline const_iterator operator-(difference_type n)
			{ return parent::operator-(n); }
			inline difference_type operator-(const const_iterator & b)
			{ return parent::operator-(b); }

			inline const_iterator & operator++()
			{ parent::operator++(); return *this; };
			inline const_iterator & operator--()
			{ parent::operator--(); return *this; };
			inline const_iterator & operator+=(const UInt n)
			{ parent::operator+=(n); return *this; }
			};
			// #endif


			// #if defined(AKANTU_CORE_CXX11)
			// template<class R> using iterator = iterator_internal<R>;
			// #else
			template < class T, class R, bool issame = is_same<T, R>::value >
			struct ConstConverterIteratorHelper {
			typedef typename Array<T>::template const_iterator<R> const_iterator;
			typedef typename Array<T>::template iterator<R> iterator;
			static inline const_iterator convert(const iterator & it) {
			return const_iterator(new R(*it, false));
			}
			};

			template < class T, class R >
			struct ConstConverterIteratorHelper<T, R, true> {
			typedef typename Array<T>::template const_iterator<R> const_iterator;
			typedef typename Array<T>::template iterator<R> iterator;
			static inline const_iterator convert(const iterator & it) {
			return const_iterator(it.data(), it.offset());
			}
			};


			template <class T, bool is_scal>
			template<typename R>
			class Array<T, is_scal>::iterator : public iterator_internal<R> {
			public:
			typedef iterator_internal<R> parent;
			typedef typename parent::value_type value_type;
			typedef typename parent::pointer pointer;
			typedef typename parent::reference reference;
			typedef typename parent::difference_type difference_type;
			typedef typename parent::iterator_category iterator_category;
			public:
			iterator() : parent() {};
			iterator(pointer_type data, UInt offset) : parent(data, offset) {};
			iterator(pointer warped) : parent(warped) {}
			iterator(const parent & it) : parent(it) {}
			// iterator(const iterator<R> & it) : parent(it) {}

			operator const_iterator<R>() {
			return ConstConverterIteratorHelper<T, R>::convert(*this);
			}

			inline iterator operator+(difference_type n)
			{ return parent::operator+(n);; }
			inline iterator operator-(difference_type n)
			{ return parent::operator-(n);; }
			inline difference_type operator-(const iterator & b)
			{ return parent::operator-(b); }

			inline iterator & operator++()
			{ parent::operator++(); return *this; };
			inline iterator & operator--()
			{ parent::operator--(); return *this; };
			inline iterator & operator+=(const UInt n)
			{ parent::operator+=(n); return *this; }
			};

			/* -------------------------------------------------------------------------- */
			template <class T, bool is_scal>
			template<typename R>
			inline Array<T, is_scal>::iterator<R> Array<T, is_scal>::erase(const iterator<R> & it) {
			T * curr = it.data();
			UInt pos = (curr - values) / nb_component;
			erase(pos);
			iterator<R> rit = it;
			return --rit;
			}


			// #endif

rAKA/src/common/aka_array_tmpl.hh273337d4079ffeatures/energy_computa…

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rAKA/src/common/aka_array_tmpl.hh
273337d4079ffeatures/energy_computa…

aka_array_tmpl.hh
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