hillclimber 0.1.6__cp313-cp313-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/tools/View.h

@@ -0,0 +1,296 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2025 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed 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.
+
+   plumed 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_tools_View_h
+#define __PLUMED_tools_View_h
+#include <limits>
+#include <type_traits>
+
+#include "Vector.h"
+
+namespace PLMD {
+namespace helpers {
+/// A way of specifying a dynamic extent for a view
+inline constexpr std::size_t dynamic_extent =
+  std::numeric_limits<std::size_t>::max();
+template <unsigned N, typename T> static constexpr void _zero(T *d) noexcept {
+  if constexpr (N == 1) {
+    d[0] = T(0);
+  } else {
+    _zero<N - 1>(d);
+    d[N - 1] = T(0);
+  }
+}
+} // namespace helpers
+
+/**A not-owning view for generic data
+
+The main idea is to have something that works like the span from c++20.
+
+View are CHEAP to copy (pointer and an integer), so it is better to pass
+them as values
+
+Can be used from PLMD::Vectors and standard types
+
+accessing the data of a PLMD::Vector as double:
+@code{.cpp}
+std::vector<PLMD::VecorGeneric<3>> v(3);
+PLMD::View<double,3> vd(&v[0][0]);
+@endcode
+
+accessing the data of a PLMD::Vector as PLMD::VectorGeneric<3>:
+@code{.cpp}
+std::vector<PLMD::VecorGeneric<3>> v(3);
+PLMD::View<PLMD::VecorGeneric<3>,3> vd(v.data());
+@endcode
+
+@todo  ctors from std::array and from iterators to parallel the span
+implementatio
+*/
+template <typename T, std::size_t N = helpers::dynamic_extent> class View {
+public:
+  using element_type = T;
+  using pointer = element_type *;
+  using iterator = pointer;
+  using const_iterator = const pointer;
+  using reference = element_type &;
+  using const_reference = const element_type &;
+
+private:
+  pointer ptr_;
+  std::size_t size_{N};
+
+public:
+  // constructor for fixed size View
+  template <size_t NN = N,
+            typename = std::enable_if_t<NN != helpers::dynamic_extent>>
+  explicit View(pointer p) noexcept : ptr_(p) {}
+  // generic constructor, works also for non fixed view (this might change)
+  View(pointer p, std::size_t const NN) noexcept : ptr_(p), size_(NN) {}
+  View(const View &) noexcept = default;
+  View(View &&) noexcept = default;
+  View &operator=(const View &) noexcept = default;
+  View &operator=(View &&) noexcept = default;
+  // returns the dimension
+  constexpr size_t size() const noexcept {
+    return size_;
+  }
+
+  /// returns the reference i-th element
+  constexpr reference operator[](size_t i) noexcept {
+    return ptr_[i];
+  }
+
+  /// returns the reference i-th element
+  constexpr const_reference operator[](size_t i) const noexcept {
+    return ptr_[i];
+  }
+
+  /// return the pointer to the data
+  constexpr pointer data() const noexcept {
+    return ptr_;
+  }
+
+  /// return a subview on consecutive elements
+  constexpr View<element_type, helpers::dynamic_extent>
+  subview(size_t offset,
+          size_t count = helpers::dynamic_extent) const noexcept {
+    /// @TODO: enforce these or accept the risk of undefined behaviour in
+    /// exchange for performance
+    // assert(offset <= size(), "subview: offset out of range");
+    // if (count != helpers::dynamic_extent) {
+    //   assert(count <= (size()-offset), "subview: count out of range");
+    // }
+    return {data() + offset,
+            count != helpers::dynamic_extent ? count : size() - offset};
+  }
+
+  /// return a subview on consecutive elements
+  template <size_t Offset, size_t Count = helpers::dynamic_extent>
+  constexpr auto subview() const noexcept {
+    // I am more or less implementing the subspan form the std
+    constexpr size_t FinalExtent =
+      (Count != helpers::dynamic_extent)
+      ? Count
+      : (N != helpers::dynamic_extent ? N - Offset
+         : helpers::dynamic_extent);
+    static_assert(Offset <= N, "subview: offset out of range");
+    if constexpr (Count != helpers::dynamic_extent) {
+      static_assert(Count <= (N - Offset), "subview: count out of range");
+    }
+    return View<T, FinalExtent> {
+      data() + Offset,
+      Count != helpers::dynamic_extent ? Count : size() - Offset
+    };
+  }
+
+  /// return a subview of specific size consecutive elements
+  template <size_t Count>
+  constexpr View<element_type, Count> subview_n(size_t offset) const noexcept {
+    /// @TODO: enforce these or accept the risk of undefined behaviour in
+    /// exchange for performance
+    // assert(offset <= size(), "subview: offset out of range");
+    // if (count != helpers::dynamic_extent) {
+    //   assert(count <= (size()-offset), "subview: count out of range");
+    // }
+    static_assert(Count <= N, "subview: count out of range");
+    return View<element_type, Count> {data() + offset};
+  }
+
+  constexpr iterator begin() noexcept {
+    return ptr_;
+  }
+
+  constexpr const_iterator begin() const noexcept {
+    return ptr_;
+  }
+
+  constexpr const_iterator cbegin() const noexcept {
+    return ptr_;
+  }
+
+  constexpr iterator end() noexcept {
+    return ptr_ + size_;
+  }
+
+  constexpr const_iterator end() const noexcept {
+    return ptr_ + size_;
+  }
+
+  constexpr const_iterator cend() const noexcept {
+    return ptr_ + size_;
+  }
+
+  void zero() noexcept {
+    if constexpr (N != helpers::dynamic_extent) {
+      LoopUnroller<N>::_zero(ptr_);
+    } else {
+      for (unsigned i = 0; i < size_; ++i) {
+        ptr_[i] = T(0);
+      }
+    }
+  }
+
+  /// assignment from a PLMD::VectorTyped of the same type
+  template <size_t M = N, typename VT, unsigned VD,
+            typename = std::enable_if_t<
+              M >= VD && std::is_same_v<T, std::remove_const_t<VT>>>>
+  auto &operator=(const VectorTyped<VT, VD> &v) noexcept {
+    // NOTE: if N==dynamic_extent and size_<VD, this is UB
+    PLMD::LoopUnroller<VD>::_copy(ptr_, v.data());
+    return *this;
+  }
+
+  /// assignment from a PLMD::VectorTyped explicitly request an eventual
+  /// conversion
+  template <size_t M = N, typename VT, unsigned VD,
+            typename = std::enable_if_t<M >= VD>>
+  auto &copyConv(const VectorTyped<VT, VD> &v) noexcept {
+    // NOTE: if N==dynamic_extent and size_<VD, this is UB
+    PLMD::LoopUnroller<VD>::_copy(ptr_, v.data());
+    return *this;
+  }
+
+  template <size_t M = N, typename VT, unsigned VD,
+            typename = std::enable_if_t<
+              M >= VD && std::is_same_v<T, std::remove_const_t<VT>>>>
+  auto &operator+=(const VectorTyped<VT, VD> &v) noexcept {
+    // NOTE: if N==dynamic_extent and size_<VD, this is UB
+    PLMD::LoopUnroller<VD>::_add(ptr_, v.data());
+    return *this;
+  }
+
+  template <size_t M = N, typename VT, unsigned VD,
+            typename = std::enable_if_t<
+              M >= VD && std::is_same_v<T, std::remove_const_t<VT>>>>
+  auto &operator-=(const VectorTyped<VT, VD> &v) noexcept {
+    // NOTE: if N==dynamic_extent and size_<VD, this is UB
+    PLMD::LoopUnroller<VD>::_sub(ptr_, v.data());
+    return *this;
+  }
+
+  template <typename TT> auto &operator*=(const TT v) noexcept {
+    if constexpr (N != helpers::dynamic_extent) {
+      PLMD::LoopUnroller<N>::_mul(ptr_, v);
+    } else {
+      for (unsigned i = 0; i < size_; ++i) {
+        ptr_[i] *= v;
+      }
+    }
+    return *this;
+  }
+
+  template <typename TT> auto &operator/=(const TT v) noexcept {
+    return operator*=(T(1.0) / v);
+  }
+  // some mathematical helper operations
+  // summed as double for precision concerns, maybe it is paranoid, maybe not
+  double modulo2() const noexcept {
+    if constexpr (N != helpers::dynamic_extent) {
+      return LoopUnroller<N>::_sum2(ptr_);
+    } else {
+      double sum = 0.0;
+      for (unsigned i = 0; i < size_; ++i) {
+        sum += ptr_[i] * ptr_[i];
+      }
+      return sum;
+    }
+  }
+
+  double modulo() const noexcept {
+    return sqrt(modulo2());
+    ;
+  }
+};
+
+template <typename T>
+VectorTyped<std::remove_const_t<T>, 3> delta(const View<T, 3> v1,
+    const View<T, 3> v2) noexcept {
+  // removing the const will improve some code interactions
+  return VectorTyped<std::remove_const_t<T>, 3> {
+    v2[0] - v1[0],
+    v2[1] - v1[1],
+    v2[2] - v1[2]
+  };
+}
+
+///Returns a complete dynamic view of a container
+///
+///The container must have defined the methods `data()` and `size()`
+///Also the container must have defined a public type `value_type`
+///For example a std::vector is compatible
+///A const std::vector is not compatible with this signature, to avoid confusion
+template <typename CT>
+constexpr View<typename CT::value_type> make_view(CT& container) {
+  return {container.data(),container.size()};
+}
+
+///Returns a complete constant dynamic view of a container
+///
+///The container must have defined the methods `data()` and `size()`
+///Also the container must have defined a public type `value_type`
+///For example a std::vector is compatible
+template <typename CT>
+constexpr View<const typename CT::value_type> make_const_view(const CT& container) {
+  return {container.data(),container.size()};
+}
+} // namespace PLMD
+#endif // __PLUMED_tools_View_h

plumed/_lib/include/plumed/tools/View2D.h

@@ -0,0 +1,100 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2025 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed 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.
+
+   plumed 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_tools_View2D_h
+#define __PLUMED_tools_View2D_h
+#include <limits>
+#include <type_traits>
+
+#include "View.h"
+
+namespace PLMD {
+
+/**A not-owning view for accessing array witha  2D interface
+
+The main idea is to have something that works like the mdspan from c++23.
+
+Views are CHEAP to copy (pointer and an integer), so it is better to pass
+them as values
+
+
+
+@todo  ctors from std::array and from iterators to parallel the span implementatio
+*/
+template <typename T, std::size_t N= helpers::dynamic_extent, std::size_t M= helpers::dynamic_extent>
+class View2D {
+public:
+  using data_type       = T;
+  using element_type    = View<data_type,M>;
+  using pointer         = data_type*;
+  using iterator        = pointer;
+  using const_iterator  = const pointer;
+  using reference       = data_type&;
+  using const_reference = const data_type&;
+private:
+  pointer ptr_;
+  std::size_t sizeN_{N};
+  std::size_t sizeM_{M};
+public:
+
+  ///constructor for fixed size View2D
+  template <size_t N_ = N, size_t M_ = M,
+            typename = std::enable_if_t<N_ != helpers::dynamic_extent && M_ != helpers::dynamic_extent>>
+  explicit View2D(pointer p) noexcept : ptr_(p) {}
+
+  ///constructor for a View2D with known second dimension at compile time
+  template <size_t N_ = N, size_t M_ = M,
+            typename = std::enable_if_t<N_ == helpers::dynamic_extent && M_ != helpers::dynamic_extent>>
+  View2D(pointer p, size_t NN) noexcept: ptr_(p), sizeN_(NN) {}
+
+  ///constructor for a View2D with all dimension known at run time
+  template <size_t N_ = N, size_t M_ = M,
+            typename = std::enable_if_t<N_ == helpers::dynamic_extent && M_ == helpers::dynamic_extent>>
+  View2D(pointer p, size_t NN, size_t MM) noexcept : ptr_(p), sizeN_(NN), sizeM_(MM) {}
+
+  View2D(const View2D&) noexcept =default;
+  View2D(View2D&&) noexcept =default;
+  View2D&operator =(const View2D&) noexcept =default;
+  View2D&operator =(View2D&&) noexcept =default;
+
+  ///returns the size of the first dimension
+  constexpr size_t size() const noexcept {
+    return sizeN_;
+  }
+
+  ///returns the View to the i-th row
+  constexpr element_type operator[](size_t i) noexcept {
+    return element_type{ptr_ + i * sizeM_,sizeM_};
+  }
+
+  ///returns the reference i-th element
+  constexpr const element_type operator[](size_t i) const noexcept {
+    return element_type{ptr_ + i * sizeM_, sizeM_};
+  }
+
+  ///return the pointer to the data
+  constexpr pointer data() const noexcept {
+    return ptr_;
+  }
+};
+
+} // namespace PLMD
+#endif // __PLUMED_tools_View2D_h

plumed/_lib/include/plumed/tools/h36.h

@@ -0,0 +1,39 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2011-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed 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.
+
+   plumed 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_tools_h36_h
+#define __PLUMED_tools_h36_h
+
+namespace PLMD {
+
+/// Tiny namespace for hybrid36 format.
+/// This namespace includes freely available tools for h36 format.
+namespace h36 {
+
+const char* hy36encode(unsigned width, int value, char* result);
+
+const char* hy36decode(unsigned width, const char* s, unsigned s_size, int* result);
+
+
+}
+
+}
+#endif

plumed/_lib/include/plumed/vatom/ActionWithVirtualAtom.h

@@ -0,0 +1,32 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2012-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed 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.
+
+   plumed 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_vatom_ActionWithVirtualAtom_h
+#define __PLUMED_vatom_ActionWithVirtualAtom_h
+#include "../core/ActionWithVirtualAtom.h"
+namespace PLMD {
+namespace vatom {
+// core/ActionWithVirtualAtom.h is left in core as it might be used in other classes
+// With this trick, PLMD::ActionWithVirtualAtom is visible as PLMD::vatom::ActionWithVirtualAtom
+using PLMD::ActionWithVirtualAtom;
+}
+}
+#endif