v0.5.0

ChangeLog.rst

@@ -14,10 +14,28 @@ Changelog
 .. Meta 
 .. ~~~~
 
+Unreleased
+-------------------------------
+Added
+~~~~~
+Changed
+~~~~~~~
+Removed
+~~~~~~~
+Bugfixes
+~~~~~~~~
+Meta 
+~~~~
+
+
 .. Version is specified in vcpkg.json, index.rst and version.hpp
 
-Unreleased
+Version 0.5.0
 -------------------------------
+
+This release introduce saddle-point finding and min->sp->min pathway finding. The concept of a generic potential was made more concrete to prevent a template explosion.
+
+
 Added
 ~~~~~
 
@@ -33,6 +51,7 @@ Changed
 - Generalised ``StepLBFGS``'s ``.newton_step()``.
 - ``Generic`` potential API + constructor changes
 - Unified minimiser, saddle finder and dimer return codes to follow C conventions (truthy on failure);
+- ``Spline`` methods clamp input.
 
 Removed
 ~~~~~~~
@@ -45,16 +64,12 @@ Bugfixes
 - Const-corrected ``Generic::gradient``.
 - Padded spline with terminator to fix-up floating point rounding errors.
 
-Meta 
-~~~~
-
 
 Version 0.4.0
 --------------
 
 This release introduces generic potentials and the first concrete potential into openFLY, EAM. The EAM implementation includes support for analytic Hessians and is fully openMP parallelised. Additionally, an efficient parallel implementation of the LBFGS minimiser is included.
 
-
 Added
 ~~~~~
 
@@ -69,8 +84,6 @@ Added
 - New ``Hessian`` class.
 - ``Frozen`` property has a tag to enable GSD IO.
 
-
-
 Changed
 ~~~~~~~
 
@@ -89,7 +102,6 @@ Bugfixes
 
 - Box (Ortho and Triclinic, valid bounds now include zero).
 
-
 Version 0.3.0
 ------------------------
 

docs/api.rst

@@ -10,8 +10,8 @@ Welcome to the libFLY API reference this serves as information for developers to
 
    api/utility.rst
    api/system.rst
-   api/io.rst
    api/neighbour.rst
+   api/io.rst
    api/potential.rst
    api/minimise.rst
    api/saddle.rst

docs/index.rst

@@ -1,4 +1,4 @@
-OpenFLY 0.4.0
+OpenFLY 0.4.x-dev
 ===================================
 
 .. toctree::

include/libfly/saddle/find.hpp

@@ -96,7 +96,7 @@ namespace fly::saddle {
       /**
        * @brief Number of simultaneous SP searches per new environment.
        */
-      int batch_size = 10;
+      int batch_size = std::min(max_failed_searches, num_threads);
       /**
        * @brief Fraction of distance between initial position and SP that dimer is displaced along its axis before minimisation.
        */

include/libfly/saddle/rotor.hpp

@@ -28,7 +28,7 @@
 /**
  * \file rotor.hpp
  *
- * @brief Class to orient a dimer.
+ * @brief Class to orient a dimer, exposes part of the ``Dimer`` classes implementation for re-use.
  */
 
 namespace fly::saddle {

include/libfly/system/VoS.hpp

@@ -60,12 +60,12 @@ namespace fly::system {
     using vector::emplace_back;
 
     /**
-     * @brief Provides an emplace_back with explicit ``matrix_t`` parameters.
+     * @brief Provides an emplace_back with explicit ``matrix_t const&`` parameters.
      */
     decltype(auto) emplace_back(typename T::matrix_t const &...args) { return vector::emplace_back(args...); }
 
     /**
-     * @brief Provides an emplace_back with explicit ``matrix_t`` parameters.
+     * @brief Provides an emplace_back with explicit ``matrix_t &&`` parameters.
      */
     decltype(auto) emplace_back(typename T::matrix_t &&...args) { return vector::emplace_back(std::move(args)...); }
   };

include/libfly/utility/spline.hpp

@@ -54,6 +54,13 @@ namespace fly {
     /**
      * @brief Interpolate tabulated function.
      *
+     * \rst
+     *
+     * .. warning::
+     *    This silently clamps ``x`` inside the tabulated region.
+     *
+     * \endrst
+     *
      * @param x Point to interpolate ``f``.
      * @return ``f(x)`` The interpolated value of the function at ``x``.
      */
@@ -65,6 +72,13 @@ namespace fly {
     /**
      * @brief Interpolate tabulated function's gradient.
      *
+     * \rst
+     *
+     * .. warning::
+     *    This silently clamps ``x`` inside the tabulated region.
+     *
+     * \endrst
+     *
      * @param x Point to interpolate ``f'``.
      * @return ``f'(x)`` The interpolated gradient of the function at ``x``.
      */
@@ -78,6 +92,9 @@ namespace fly {
      *
      * \rst
      *
+     * .. warning::
+     *    This silently clamps ``x`` inside the tabulated region.
+     *
      * .. note::
      *    This may not be continuous or smooth.
      *
@@ -105,13 +122,9 @@ namespace fly {
       //
       ASSERT(x >= 0, "x={}, not less than zero", x);
 
-      auto i = static_cast<std::size_t>(x * m_inv_dx);
-
-      // Could clamp this value:  
-
-      i = std::min(i, m_spines.size() - 1);
+      auto i = std::min(static_cast<std::size_t>(x * m_inv_dx), m_spines.size() - 1);
 
-      ASSERT(i < m_spines.size(), "x={} is outside tabulated region with i={}, len={}", x, i, m_spines.size());
+      //   ASSERT(i < m_spines.size(), "x={} is outside tabulated region with i={}, len={}", x, i, m_spines.size());
 
       return {x - static_cast<double>(i) * m_dx, m_spines[i]};
     }

include/libfly/utility/version.hpp

@@ -21,5 +21,5 @@
  */
 
 #define FLY_VERSION_MAJOR 0  ///< The major version umber.
-#define FLY_VERSION_MINOR 4  ///< The minor version umber.
+#define FLY_VERSION_MINOR 5  ///< The minor version umber.
 #define FLY_VERSION_PATCH 0  ///< The patch umber.

vcpkg.json

@@ -1,6 +1,6 @@
 {
     "name": "openfly",
-    "version-semver": "0.4.0",
+    "version-semver": "0.5.0",
     "dependencies": [
         {
             "name": "fmt",