Update release notes for gmx msd and clear some TODOs

[alexxy/gromacs.git] / src / gromacs / trajectoryanalysis / modules / msd.cpp

diff --git a/src/gromacs/trajectoryanalysis/modules/msd.cpp b/src/gromacs/trajectoryanalysis/modules/msd.cpp
index 52a89476efae0db5990208cfa80052461d3b3bf0..0a0dd25616e296690a6b9e50689926f763388b46 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/msd.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/msd.cpp
@@ -171,19 +171,22 @@ inline double calcSingleSquaredDistance(const RVec c1, const RVec c2)
     const DVec firstCoords  = c1.toDVec();
     const DVec secondCoords = c2.toDVec();
     double     result       = 0;
-    if constexpr (x) // NOLINT // NOLINTNEXTLINE
+    if constexpr (x)
     {
         result += (firstCoords[XX] - secondCoords[XX]) * (firstCoords[XX] - secondCoords[XX]);
     }
-    if constexpr (y) // NOLINT // NOLINTNEXTLINE
+    // NOLINTNEXTLINE(readability-misleading-indentation) remove when clang-tidy-13 is required
+    if constexpr (y)
     {
         result += (firstCoords[YY] - secondCoords[YY]) * (firstCoords[YY] - secondCoords[YY]);
     }
-    if constexpr (z) // NOLINT // NOLINTNEXTLINE
+    // NOLINTNEXTLINE(readability-misleading-indentation) remove when clang-tidy-13 is required
+    if constexpr (z)
     {
         result += (firstCoords[ZZ] - secondCoords[ZZ]) * (firstCoords[ZZ] - secondCoords[ZZ]);
     }
-    return result; // NOLINT
+    // NOLINTNEXTLINE(readability-misleading-indentation) remove when clang-tidy-13 is required
+    return result;
 }
 
 /*! \brief Calculate average displacement between sets of points
@@ -281,10 +284,7 @@ public:
     MsdCoordinateManager(const int                    numAtoms,
                          ArrayRef<const MoleculeData> molecules,
                          ArrayRef<const int>          moleculeIndexMapping) :
-        current_(numAtoms),
-        previous_(numAtoms),
-        molecules_(molecules),
-        moleculeIndexMapping_(moleculeIndexMapping)
+        current_(numAtoms), previous_(numAtoms), molecules_(molecules), moleculeIndexMapping_(moleculeIndexMapping)
     {
     }
     /*! \brief Prepares coordinates for the current frame.
@@ -391,12 +391,9 @@ struct MsdGroupData
 
 /*! \brief Implements the gmx msd module
  *
- * \todo Implement -(no)mw. Right now, all calculations are mass-weighted with -mol, and not otherwise
  * \todo Implement -tensor for full MSD tensor calculation
  * \todo Implement -rmcomm for total-frame COM removal
  * \todo Implement -pdb for molecule B factors
- * \todo Implement -maxtau option proposed at https://gitlab.com/gromacs/gromacs/-/issues/3870
- * \todo Update help text as options are added and clarifications decided on at https://gitlab.com/gromacs/gromacs/-/issues/3869
  */
 class Msd : public TrajectoryAnalysisModule
 {