Diffusion akantu (bugfixes/39-the-python-example-for-phasefield-are-broken-due-to-a-change-to-setintegrationscheme) Browse

39-the-python…

Last Change

Raw File

aka_array.hh
View Options

			/**
			* @file aka_array.hh
			*
			* @author Till Junge <till.junge@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Fri Jun 18 2010
			* @date last modification: Sun Nov 22 2020
			*
			* @brief Array container for Akantu This container differs from the
			* std::vector from the fact it as 2 dimensions a main dimension and the size
			* stored per entries
			*
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2021 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/>.
			*
			*/

			/* -------------------------------------------------------------------------- */
			#include "aka_common.hh"
			#include "aka_types.hh"
			/* -------------------------------------------------------------------------- */
			#include <typeinfo>
			#include <vector>
			/* -------------------------------------------------------------------------- */

			/* -------------------------------------------------------------------------- */
			#ifndef AKANTU_ARRAY_HH_
			#define AKANTU_ARRAY_HH_

			namespace akantu {

			/// class that afford to store vectors in static memory
			// NOLINTNEXTLINE(cppcoreguidelines-special-member-functions)
			class ArrayBase {
			/* ------------------------------------------------------------------------ */
			/* Constructors/Destructors */
			/* ------------------------------------------------------------------------ */
			public:
			explicit ArrayBase(const ID & id = "") : id(id) {}
			ArrayBase(const ArrayBase & other, const ID & id = "") {
			this->id = (id.empty()) ? other.id : id;
			}

			ArrayBase(ArrayBase && other) = default;
			ArrayBase & operator=(const ArrayBase & other) = default;
			ArrayBase & operator=(ArrayBase && other) noexcept = default;

			virtual ~ArrayBase() = default;

			/* ------------------------------------------------------------------------ */
			/* Methods */
			/* ------------------------------------------------------------------------ */
			public:
			/// get the amount of space allocated in bytes
			virtual UInt getMemorySize() const = 0;

			// changed empty to match std::vector empty
			inline bool empty() const __attribute__((warn_unused_result)) {
			return size_ == 0;
			}

			/// function to print the containt of the class
			virtual void printself(std::ostream & stream, int indent = 0) const = 0;

			/* ------------------------------------------------------------------------ */
			/* Accessors */
			/* ------------------------------------------------------------------------ */
			public:
			/// Get the Size of the Array
			UInt size() const { return size_; }
			/// Get the number of components
			AKANTU_GET_MACRO(NbComponent, nb_component, UInt);
			/// Get the name of th array
			AKANTU_GET_MACRO(ID, id, const ID &);
			/// Set the name of th array
			AKANTU_SET_MACRO(ID, id, const ID &);

			/* ------------------------------------------------------------------------ */
			/* Class Members */
			/* ------------------------------------------------------------------------ */
			protected:
			/// id of the vector
			ID id;

			/// the size used
			UInt size_{0};

			/// number of components
			UInt nb_component{1};
			};

			/* -------------------------------------------------------------------------- */
			namespace {
			template <std::size_t dim, typename T> struct IteratorHelper {};

			template <typename T> struct IteratorHelper<0, T> { using type = T; };
			template <typename T> struct IteratorHelper<1, T> { using type = Vector<T>; };
			template <typename T> struct IteratorHelper<2, T> { using type = Matrix<T>; };
			template <typename T> struct IteratorHelper<3, T> {
			using type = Tensor3<T>;
			};

			template <std::size_t dim, typename T>
			using IteratorHelper_t = typename IteratorHelper<dim, T>::type;
			} // namespace

			/* -------------------------------------------------------------------------- */
			/* Memory handling layer */
			/* -------------------------------------------------------------------------- */
			enum class ArrayAllocationType {
			_default,
			_pod,
			};

			template <typename T>
			struct ArrayAllocationTrait
			: public std::conditional_t<
			std::is_scalar<T>::value,
			std::integral_constant<ArrayAllocationType,
			ArrayAllocationType::_pod>,
			std::integral_constant<ArrayAllocationType,
			ArrayAllocationType::_default>> {};

			/* -------------------------------------------------------------------------- */
			template <typename T,
			ArrayAllocationType allocation_trait = ArrayAllocationTrait<T>::value>
			class ArrayDataLayer : public ArrayBase {
			public:
			using value_type = T;
			using reference = value_type &;
			using pointer_type = value_type *;
			using const_reference = const value_type &;

			public:
			~ArrayDataLayer() override = default;

			/// Allocation of a new vector
			explicit ArrayDataLayer(UInt size = 0, UInt nb_component = 1,
			const ID & id = "");

			/// Allocation of a new vector with a default value
			ArrayDataLayer(UInt size, UInt nb_component, const_reference value,
			const ID & id = "");

			/// Copy constructor (deep copy)
			ArrayDataLayer(const ArrayDataLayer & vect, const ID & id = "");

			/// Copy constructor (deep copy)
			explicit ArrayDataLayer(const std::vector<value_type> & vect);

			// copy operator
			ArrayDataLayer & operator=(const ArrayDataLayer & other);

			// move constructor
			ArrayDataLayer(ArrayDataLayer && other) noexcept = default;

			// move assign
			ArrayDataLayer & operator=(ArrayDataLayer && other) noexcept = default;

			protected:
			// deallocate the memory
			virtual void deallocate() {}

			// allocate the memory
			virtual void allocate(UInt size, UInt nb_component);

			// allocate and initialize the memory
			virtual void allocate(UInt size, UInt nb_component, const T & value);

			public:
			/// append a tuple of size nb_component containing value
			inline void push_back(const_reference value);
			/// append a vector
			// inline void push_back(const value_type new_elem[]);

			/// append a Vector or a Matrix
			template <template <typename> class C,
			typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
			aka::is_tensor_proxy<C<T>>::value>>
			inline void push_back(const C<T> & new_elem);

			/// changes the allocated size but not the size, if new_size = 0, the size is
			/// set to min(current_size and reserve size)
			virtual void reserve(UInt size, UInt new_size = UInt(-1));

			/// change the size of the Array
			virtual void resize(UInt size);

			/// change the size of the Array and initialize the values
			virtual void resize(UInt size, const T & val);

			/// get the amount of space allocated in bytes
			inline UInt getMemorySize() const override;

			/// Get the real size allocated in memory
			inline UInt getAllocatedSize() const;

			/// give the address of the memory allocated for this vector
			T * storage() const { return values; };

			protected:
			/// allocation type agnostic data access
			T * values{nullptr};

			/// data storage
			std::vector<T> data_storage;
			};

			/* -------------------------------------------------------------------------- */
			/* Actual Array */
			/* -------------------------------------------------------------------------- */
			template <typename T, bool is_scal> class Array : public ArrayDataLayer<T> {
			private:
			using parent = ArrayDataLayer<T>;
			/* ------------------------------------------------------------------------ */
			/* Constructors/Destructors */
			/* ------------------------------------------------------------------------ */
			public:
			using value_type = typename parent::value_type;
			using reference = typename parent::reference;
			using pointer_type = typename parent::pointer_type;
			using const_reference = typename parent::const_reference;
			using array_type = Array<T>;

			~Array() override;

			Array() : Array(0){};

			/// Allocation of a new vector
			explicit Array(UInt size, UInt nb_component = 1, const ID & id = "");

			/// Allocation of a new vector with a default value
			explicit Array(UInt size, UInt nb_component, const_reference value,
			const ID & id = "");

			/// Copy constructor
			Array(const Array & vect, const ID & id = "");

			/// Copy constructor (deep copy)
			explicit Array(const std::vector<T> & vect);

			// copy operator
			Array & operator=(const Array & other);

			// move constructor
			Array(Array && other) noexcept = default;

			// move assign
			Array & operator=(Array && other) noexcept = default;

			/* ------------------------------------------------------------------------ */
			/* Iterator */
			/* ------------------------------------------------------------------------ */
			/// \todo protected: does not compile with intel check why
			public:
			template <class R, class it, class IR = R,
			bool is_tensor_ = aka::is_tensor<std::decay_t<R>>::value>
			class iterator_internal;

			public:
			/* ------------------------------------------------------------------------ */

			/* ------------------------------------------------------------------------ */
			template <typename R = T> class const_iterator;
			template <typename R = T> class iterator;

			/* ------------------------------------------------------------------------ */

			/// iterator for Array of nb_component = 1
			using scalar_iterator = iterator<T>;
			/// const_iterator for Array of nb_component = 1
			using const_scalar_iterator = const_iterator<T>;

			/// iterator returning Vectors of size n on entries of Array with
			/// nb_component = n
			using vector_iterator = iterator<Vector<T>>;
			/// const_iterator returning Vectors of n size on entries of Array with
			/// nb_component = n
			using const_vector_iterator = const_iterator<Vector<T>>;

			/// iterator returning Matrices of size (m, n) on entries of Array with
			/// nb_component = m*n
			using matrix_iterator = iterator<Matrix<T>>;
			/// const iterator returning Matrices of size (m, n) on entries of Array with
			/// nb_component = m*n
			using const_matrix_iterator = const_iterator<Matrix<T>>;

			/// iterator returning Tensor3 of size (m, n, k) on entries of Array with
			/// nb_component = mnk
			using tensor3_iterator = iterator<Tensor3<T>>;
			/// const iterator returning Tensor3 of size (m, n, k) on entries of Array
			/// with nb_component = mnk
			using const_tensor3_iterator = const_iterator<Tensor3<T>>;

			/* ------------------------------------------------------------------------ */
			template <typename... Ns> inline decltype(auto) begin(Ns &&... n);
			template <typename... Ns> inline decltype(auto) end(Ns &&... n);

			template <typename... Ns> inline decltype(auto) begin(Ns &&... n) const;
			template <typename... Ns> inline decltype(auto) end(Ns &&... n) const;

			template <typename... Ns> inline decltype(auto) begin_reinterpret(Ns &&... n);
			template <typename... Ns> inline decltype(auto) end_reinterpret(Ns &&... n);

			template <typename... Ns>
			inline decltype(auto) begin_reinterpret(Ns &&... n) const;
			template <typename... Ns>
			inline decltype(auto) end_reinterpret(Ns &&... n) const;

			/* ------------------------------------------------------------------------ */
			/* Methods */
			/* ------------------------------------------------------------------------ */
			public:
			/// search elem in the vector, return the position of the first occurrence or
			/// -1 if not found
			UInt find(const_reference elem) const;

			/// @see Array::find(const_reference elem) const
			// UInt find(T elem[]) const;

			/// append a value to the end of the Array
			inline void push_back(const_reference value) { parent::push_back(value); }

			/// append a Vector or a Matrix
			template <template <typename> class C,
			typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
			aka::is_tensor_proxy<C<T>>::value>>
			inline void push_back(const C<T> & new_elem) {
			parent::push_back(new_elem);
			}

			/// append the content of the iterator at the end of the Array
			template <typename Ret> inline void push_back(const iterator<Ret> & it) {
			push_back(*it);
			}

			/// erase the value at position i
			inline void erase(UInt i);
			/// ask Nico, clarify
			template <typename R> inline iterator<R> erase(const iterator<R> & it);

			/// @see Array::find(const_reference elem) const
			template <template <typename> class C,
			typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
			aka::is_tensor_proxy<C<T>>::value>>
			inline UInt find(const C<T> & elem);

			/// set all entries of the array to the value t
			/// @param t value to fill the array with
			inline void set(T t) {
			std::fill_n(this->values, this->size_ * this->nb_component, t);
			}

			/// set the array to T{}
			inline void zero() { this->set({}); }

			/// resize the array to 0
			inline void clear() { this->resize(0); }

			/// set all tuples of the array to a given vector or matrix
			/// @param vm Matrix or Vector to fill the array with
			template <template <typename> class C,
			typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
			aka::is_tensor_proxy<C<T>>::value>>
			inline void set(const C<T> & vm);

			/// Append the content of the other array to the current one
			void append(const Array<T> & other);

			/// copy another Array in the current Array, the no_sanity_check allows you to
			/// force the copy in cases where you know what you do with two non matching
			/// Arrays in terms of n
			void copy(const Array<T, is_scal> & other, bool no_sanity_check = false);

			/// function to print the containt of the class
			void printself(std::ostream & stream, int indent = 0) const override;

			/* ------------------------------------------------------------------------ */
			/* Operators */
			/* ------------------------------------------------------------------------ */
			public:
			/// substraction entry-wise
			Array<T, is_scal> & operator-=(const Array<T, is_scal> & other);
			/// addition entry-wise
			Array<T, is_scal> & operator+=(const Array<T, is_scal> & other);
			/// multiply evry entry by alpha
			Array<T, is_scal> & operator*=(const T & alpha);

			/// check if the array are identical entry-wise
			bool operator==(const Array<T, is_scal> & other) const;
			/// @see Array::operator==(const Array<T, is_scal> & other) const
			bool operator!=(const Array<T, is_scal> & other) const;

			/// return a reference to the j-th entry of the i-th tuple
			inline reference operator()(UInt i, UInt j = 0);
			/// return a const reference to the j-th entry of the i-th tuple
			inline const_reference operator()(UInt i, UInt j = 0) const;

			/// return a reference to the ith component of the 1D array
			inline reference operator[](UInt i);
			/// return a const reference to the ith component of the 1D array
			inline const_reference operator[](UInt i) const;
			};

			/* -------------------------------------------------------------------------- */
			/* Inline Functions Array<T, is_scal> */
			/* -------------------------------------------------------------------------- */
			template <typename T, bool is_scal>
			inline std::ostream & operator<<(std::ostream & stream,
			const Array<T, is_scal> & _this) {
			_this.printself(stream);
			return stream;
			}

			/* -------------------------------------------------------------------------- */
			/* Inline Functions ArrayBase */
			/* -------------------------------------------------------------------------- */
			inline std::ostream & operator<<(std::ostream & stream,
			const ArrayBase & _this) {
			_this.printself(stream);
			return stream;
			}

			} // namespace akantu

			#include "aka_array_tmpl.hh"

			#endif /* AKANTU_ARRAY_HH_ */

rAKA/src/common/aka_array.hhbf256d3a02cdbugfixes/39-the-python…

aka_array.hhView Options

rAKA/src/common/aka_array.hh
bf256d3a02cdbugfixes/39-the-python…

aka_array.hh
View Options