Fixed some cppcheck issues in code

plumed · Mar 6, 2025 · a5bf885 · a5bf885 · PlumedBot · Mar 6, 2025
1 parent bea8632
commit a5bf885
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Showing 6 changed files with 36 additions and 17 deletions.
diff --git a/src/secondarystructure/SecondaryStructureBase.cpp b/src/secondarystructure/SecondaryStructureBase.cpp
@@ -20,12 +20,3 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "SecondaryStructureBase.h"
-
-//+PLUMEDOC MCOLVAR SECONDARY_STRUCTURE_RMSD
-/*
-Calclulate the distance between segments of a protein and a reference structure of interest
-
-\par Examples
-
-*/
-//+ENDPLUMEDOC
diff --git a/src/secondarystructure/SecondaryStructureDRMSD.cpp b/src/secondarystructure/SecondaryStructureDRMSD.cpp
@@ -23,6 +23,15 @@
 #include "core/ActionRegister.h"
 #include "tools/Matrix.h"
 
+//+PLUMEDOC MCOLVAR SECONDARY_STRUCTURE_DRMSD
+/*
+Calclulate the distance between segments of a protein and a reference structure of interest
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace secondarystructure {
 
@@ -41,7 +50,7 @@ class SecondaryStructureDRMSDInput {
 /// The atoms involved in each of the secondary structure segments
   Matrix<unsigned> colvar_atoms;
   static void calculateDistance( unsigned n, bool noderiv, const SecondaryStructureDRMSDInput& actiondata, const std::vector<Vector>& pos, ColvarOutput& output );
-  void setReferenceStructure( std::string type, double bondlength, std::vector<Vector>& structure );
+  void setReferenceStructure( const std::string& type, double bondlength, std::vector<Vector>& structure );
   SecondaryStructureDRMSDInput& operator=( const SecondaryStructureDRMSDInput& m ) {
     natoms = m.natoms;
     nstructures = m.nstructures;
@@ -62,7 +71,7 @@ class SecondaryStructureDRMSDInput {
 typedef SecondaryStructureBase<SecondaryStructureDRMSDInput> colv;
 PLUMED_REGISTER_ACTION(colv,"SECONDARY_STRUCTURE_DRMSD");
 
-void SecondaryStructureDRMSDInput::setReferenceStructure( std::string type, double bondlength, std::vector<Vector>& structure ) {
+void SecondaryStructureDRMSDInput::setReferenceStructure( const std::string& type, double bondlength, std::vector<Vector>& structure ) {
   std::map<std::pair<unsigned,unsigned>, double> targets;
   for(unsigned i=0; i<structure.size()-1; ++i) {
     for(unsigned j=i+1; j<structure.size(); ++j) {

diff --git a/src/secondarystructure/SecondaryStructureRMSD.cpp b/src/secondarystructure/SecondaryStructureRMSD.cpp
@@ -23,6 +23,15 @@
 #include "core/ActionRegister.h"
 #include "tools/RMSD.h"
 
+//+PLUMEDOC MCOLVAR SECONDARY_STRUCTURE_RMSD
+/*
+Calclulate the distance between segments of a protein and a reference structure of interest
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace secondarystructure {
 
@@ -41,7 +50,7 @@ class SecondaryStructureRMSDInput {
 /// The atoms involved in each of the secondary structure segments
   Matrix<unsigned> colvar_atoms;
   static void calculateDistance( unsigned n, bool noderiv, const SecondaryStructureRMSDInput& actiondata, const std::vector<Vector>& pos, ColvarOutput& output );
-  void setReferenceStructure( std::string type, double bondlength, std::vector<Vector>& structure );
+  void setReferenceStructure( const std::string& type, double bondlength, std::vector<Vector>& structure );
   SecondaryStructureRMSDInput& operator=( const SecondaryStructureRMSDInput& m ) {
     natoms = m.natoms;
     nstructures = m.nstructures;
@@ -59,7 +68,7 @@ class SecondaryStructureRMSDInput {
 typedef SecondaryStructureBase<SecondaryStructureRMSDInput> colv;
 PLUMED_REGISTER_ACTION(colv,"SECONDARY_STRUCTURE_RMSD");
 
-void SecondaryStructureRMSDInput::setReferenceStructure( std::string type, double bondlength, std::vector<Vector>& structure ) {
+void SecondaryStructureRMSDInput::setReferenceStructure( const std::string& type, double bondlength, std::vector<Vector>& structure ) {
   Vector center;
   std::vector<double> align( structure.size(), 1.0 ), displace( structure.size(), 1.0 );
   for(unsigned i=0; i<structure.size(); ++i) {

diff --git a/src/volumes/VolumeBetweenContours.cpp b/src/volumes/VolumeBetweenContours.cpp
@@ -93,6 +93,8 @@ class VolumeInEnvelope {
     std::string errors;
     sfunc.set(sfunc_str, errors);
     switchingFunction.set("GAUSSIAN R_0=1.0 NOSTRETCH", errors );
+    natoms_in_list = m.natoms_in_list;
+    natoms_per_list = m.natoms_per_list;
     return *this;
   }
   static void calculateNumberInside( const VolumeInput& input, const VolumeInEnvelope& actioninput, VolumeOutput& output );

diff --git a/src/volumes/VolumeCavity.cpp b/src/volumes/VolumeCavity.cpp
@@ -124,18 +124,22 @@ class VolumeCavity {
   std::vector<Vector> dlbi, dlcross, dlperp;
   std::vector<Tensor> dbi, dcross, dperp;
   static void registerKeywords( Keywords& keys );
-  VolumeCavity() : dlbi(4), dlcross(4), dlperp(4), dbi(3), dcross(3), dperp(3) {}
+  VolumeCavity() : jacob_det(0), len_bi(0), len_cross(0), len_perp(0), sigma(0), dlbi(4), dlcross(4), dlperp(4), dbi(3), dcross(3), dperp(3) {}
   void setupRegions( ActionVolume<VolumeCavity>* action, const Pbc& pbc, const std::vector<Vector>& positions );
   void parseInput( ActionVolume<VolumeCavity>* action );
   static void parseAtoms( ActionVolume<VolumeCavity>* action, std::vector<AtomNumber>& atoms );
   VolumeCavity& operator=( const VolumeCavity& m ) {
+    jacob_det=m.jacob_det;
+    len_bi=m.len_bi;
+    len_cross=m.len_cross;
+    len_perp=m.len_perp;
+    sigma=m.sigma;
     dlbi.resize(4);
     dlcross.resize(4);
     dlperp.resize(4);
     dbi.resize(3);
     dcross.resize(3);
     dperp.resize(3);
-    sigma = m.sigma;
     kerneltype=m.kerneltype;
     return *this;
   }

diff --git a/src/volumes/VolumeTetrapore.cpp b/src/volumes/VolumeTetrapore.cpp
@@ -132,18 +132,22 @@ class VolumeTetrapore {
   std::vector<Vector> dlbi, dlcross, dlperp;
   std::vector<Tensor> dbi, dcross, dperp;
   static void registerKeywords( Keywords& keys );
-  VolumeTetrapore() : dlbi(4), dlcross(4), dlperp(4), dbi(3), dcross(3), dperp(3) {}
+  VolumeTetrapore() : jacob_det(0), len_bi(0), len_cross(0), len_perp(0), sigma(0), dlbi(4), dlcross(4), dlperp(4), dbi(3), dcross(3), dperp(3) {}
   void setupRegions( ActionVolume<VolumeTetrapore>* action, const Pbc& pbc, const std::vector<Vector>& positions );
   void parseInput( ActionVolume<VolumeTetrapore>* action );
   static void parseAtoms( ActionVolume<VolumeTetrapore>* action, std::vector<AtomNumber>& atoms );
   VolumeTetrapore& operator=( const VolumeTetrapore& m ) {
+    jacob_det=m.jacob_det;
+    len_bi=m.len_bi;
+    len_cross=m.len_cross;
+    len_perp=m.len_perp;
+    sigma=m.sigma;
     dlbi.resize(4);
     dlcross.resize(4);
     dlperp.resize(4);
     dbi.resize(3);
     dcross.resize(3);
     dperp.resize(3);
-    sigma = m.sigma;
     kerneltype=m.kerneltype;
     return *this;
   }