Nblib doc fixes

Update some doc strings to make future merges more concise.

diff --git a/api/nblib/listed_forces/calculator.h b/api/nblib/listed_forces/calculator.h
index d5c149367b447774e11e992ffca45ffc8ed95217..7017862aa690dcb98a09608e82dc3b9d53df2101 100644 (file)
--- a/api/nblib/listed_forces/calculator.h
+++ b/api/nblib/listed_forces/calculator.h
@@ -95,17 +95,13 @@ public:
      */
     void compute(gmx::ArrayRef<const Vec3> coordinates, gmx::ArrayRef<Vec3> forces, bool usePbc = false);
 
-    //! Alternative overload with the energies in an output buffer
+    //! \brief Alternative overload with the energies in an output buffer
     void compute(gmx::ArrayRef<const Vec3> coordinates,
                  gmx::ArrayRef<Vec3>       forces,
                  EnergyType&               energies,
                  bool                      usePbc = false);
 
-    /*! \brief We need to declare the destructor here to move the (still default) implementation
-     *  to the .cpp file. Omitting this declaration would mean an inline destructor
-     *  which can't compile because the unique_ptr dtor needs ~ForceBuffer, which is not available
-     * here because it's incomplete.
-     */
+    //! \brief default, but moved to separate compilation unit
     ~ListedForceCalculator();
 
 private:

diff --git a/api/nblib/listed_forces/conversions.hpp b/api/nblib/listed_forces/conversions.hpp
index fc79786029c50462e71bdb26bf673eb0ee7bd4f1..3c8e9783e8ff6260aaad7b6a864185f4dee8ffc3 100644 (file)
--- a/api/nblib/listed_forces/conversions.hpp
+++ b/api/nblib/listed_forces/conversions.hpp
@@ -58,7 +58,7 @@ namespace nblib
 
 /*! this trait maps nblib InteractionTypes to the corresponding gmx enum
  *
- * @tparam InteractionType
+ * \tparam InteractionType
  */
 template<class InteractionType>
 struct ListedIndex
@@ -124,6 +124,7 @@ void transferParameters([[maybe_unused]] const InteractionData& interactionData,
 {
 }
 
+//! \brief Harmonic bond parameter conversion function
 template<>
 void transferParameters(const ListedTypeData<HarmonicBondType>& interactions, gmx_ffparams_t& gmx_params)
 {
@@ -136,6 +137,7 @@ void transferParameters(const ListedTypeData<HarmonicBondType>& interactions, gm
     }
 }
 
+//! \brief Harmonic angle parameter conversion function
 template<>
 void transferParameters(const ListedTypeData<HarmonicAngle>& interactions, gmx_ffparams_t& gmx_params)
 {
@@ -148,6 +150,7 @@ void transferParameters(const ListedTypeData<HarmonicAngle>& interactions, gmx_f
     }
 }
 
+//! \brief Proper dihedral parameter conversion function
 template<>
 void transferParameters(const ListedTypeData<ProperDihedral>& interactions, gmx_ffparams_t& gmx_params)
 {

diff --git a/api/nblib/particlesequencer.cpp b/api/nblib/particlesequencer.cpp
index 7bb98bed165eaf963b75cd4cdf9ffa7eb4e628c7..a907718f72a505263155d3838be57a89b8fb7d92 100644 (file)
--- a/api/nblib/particlesequencer.cpp
+++ b/api/nblib/particlesequencer.cpp
@@ -62,7 +62,6 @@ int ParticleSequencer::operator()(const MoleculeName& moleculeName,
     }
     catch (const std::out_of_range& outOfRange)
     {
-        // TODO: use string format function once we have it
         if (moleculeName.value() == residueName.value())
         {
             printf("No particle %s in residue %s in molecule %s found\n",

diff --git a/api/nblib/particletype.h b/api/nblib/particletype.h
index f5d86bb39e685c839614280021eb7f49981c590b..da43f972ce09e8e79ad45c1ad20d069d6f477e3e 100644 (file)
--- a/api/nblib/particletype.h
+++ b/api/nblib/particletype.h
@@ -62,7 +62,7 @@ using ParticleTypeName = StrongType<std::string, struct ParticleTypeNameParamete
 //! Named type for particle mass
 using Mass = StrongType<real, struct MassParameter>;
 
-// Shorthand for a map used for looking up non-bonded parameters using particle types
+//! Shorthand for a map used for looking up non-bonded parameters using particle types
 //! Named type for the C6 parameter in the Lennard-Jones potential
 using C6 = StrongType<real, struct C6Parameter>;
 //! Named type for the C12 parameter in the Lennard-Jones potential

diff --git a/api/nblib/simulationstate.cpp b/api/nblib/simulationstate.cpp
index dbbfa10c2746c8f09fa6ca1f79eb18985567168b..7b8be49da9fb279214949c058a8a3c404e590f10 100644 (file)
--- a/api/nblib/simulationstate.cpp
+++ b/api/nblib/simulationstate.cpp
@@ -51,6 +51,7 @@
 #include "nblib/simulationstate.h"
 #include "nblib/simulationstateimpl.h"
 #include "nblib/util/setup.h"
+#include "nblib/vector.h"
 
 namespace nblib
 {

diff --git a/api/nblib/simulationstate.h b/api/nblib/simulationstate.h
index 1beb3b17d316a158ef299fdf30821c91e8411f03..944b00ee651cbcec3361040607dd69b4a4fc7767 100644 (file)
--- a/api/nblib/simulationstate.h
+++ b/api/nblib/simulationstate.h
@@ -49,9 +49,9 @@
 #include <memory>
 #include <vector>
 
-#include "box.h"
-#include "topology.h"
-#include "vector.h"
+#include "nblib/box.h"
+#include "nblib/topology.h"
+#include "nblib/vector.h"
 
 namespace nblib
 {