fixes for -Wextra -Wpedantic -Wshadow -Wconversion

README.md

@@ -3,40 +3,16 @@
 [![Build Status](https://travis-ci.org/votca/csgapps.svg?branch=master)](https://travis-ci.org/votca/csgapps)
 [![pipeline status](https://gitlab.com/votca/csgapps/badges/master/pipeline.svg)](https://gitlab.com/votca/csgapps/commits/master)
 
-This repository contains some small analysis programs which are written based on the votca_csg framework
+This repository contains some small analysis programs which are written based on the votca csg framework
 
 # Programs
 
-* __radii__
-
-  calculate gyration radius + hydrodynamic radius of a molecule or a set of molecules
-
-* __sphericalorder__
-
-  calculates a spherical order parameter i.e. the distribution of e_r\*u where e_r is the unit vector from
-  a reference molecule to the solvent molecules and u is the principle axis of inertia of the solvent molecule
-
-* __fluctuations__
-
-  calculate the number density fluctuations in subvolumes. Subvolumes are either cubic slabs along one of the
-  sim box axis or speherical subvolumes around a solute
-
-* __orientcorr__
-
-  calculates the distance dependent orientational correlation function of a polymer melt
-
-* __part_dist__
-
-  outputs the time-averaged number of particles, listed by particle types (was a part of csg before)
-
-* __partial_rdf__
-
-  calculates the rdf in a spherical subvolume 
-
-* __traj_force__
-
-  add/subtracts reference forces from a given trajectory and stores in a new trajectory
-
-
+*   _radii_: calculate gyration radius + hydrodynamic radius of a molecule or a set of molecules
+*   _sphericalorder_: calculates a spherical order parameter i.e. the distribution of e\_r\*u where e\_r is the unit vector from a reference molecule to the solvent molecules and u is the principle axis of inertia of the solvent molecule
+*   _fluctuations_: calculate the number density fluctuations in subvolumes. Subvolumes are either cubic slabs along one of the sim box axis or speherical subvolumes around a solute
+*   _orientcorr_: calculates the distance dependent orientational correlation function of a polymer melt
+*   _part_dist_: outputs the time-averaged number of particles, listed by particle types (was a part of csg before)
+*   _partial\_rdf_: calculates the rdf in a spherical subvolume
+*   _traj\_force_: add/subtracts reference forces from a given trajectory and stores in a new trajectory
 
 To add your own program just create a new folder and put your *.cc files in there

fluctuations/fluctuations.cc

@@ -16,16 +16,11 @@
  */
 
 #include <boost/program_options.hpp>
-#include <fstream>
-#include <iostream>
-#include <math.h>
-#include <stdlib.h>
 #include <votca/csg/cgengine.h>
 #include <votca/csg/csgapplication.h>
-#include <votca/tools/average.h>
+#include <votca/tools/histogramnew.h>
 #include <votca/tools/tokenizer.h>
 
-// using namespace votca::tools;
 using namespace std;
 using namespace votca::csg;
 
@@ -77,7 +72,7 @@ class CsgFluctuations : public CsgApplication {
   bool DoTrajectory() override { return true; }
   bool DoMapping() override { return true; }
 
-  void BeginEvaluate(Topology *top, Topology *top_atom) override {
+  void BeginEvaluate(Topology *top, Topology *) override {
     _filter = OptionsMap()["filter"].as<string>();
     _refmol = OptionsMap()["refmol"].as<string>();
     _rmin = OptionsMap()["rmin"].as<double>();
@@ -102,17 +97,11 @@ class CsgFluctuations : public CsgApplication {
       cout << "Doing slabs along  z-axis" << endl;
       _dim = 2;
     } else {
-      cout << "Unrecognized geometry option. (sphere|x|y|z)" << endl;
-      exit(0);
+      throw std::runtime_error("Unrecognized geometry option. (sphere|x|y|z)");
     }
 
-    _N_avg = new double[_nbins];
-    _N_sq_avg = new double[_nbins];
-    N = new int[_nbins];
-    for (int i = 0; i < _nbins; i++) {
-      _N_avg[i] = 0;
-      _N_sq_avg[i] = 0;
-    }
+    _N_avg = Eigen::VectorXd::Zero(_nbins);
+    _N_sq_avg = Eigen::VectorXd::Zero(_nbins);
 
     if (_do_spherical) {
       cout << "Calculating fluctions for " << _rmin << "<r<" << _rmax;
@@ -125,17 +114,14 @@ class CsgFluctuations : public CsgApplication {
 
     if (_refmol == "" && _do_spherical) {
       Eigen::Matrix3d box = top->getBox();
-      Eigen::Vector3d a = box.col(0);
-      Eigen::Vector3d b = box.col(1);
-      Eigen::Vector3d c = box.col(2);
-      _ref = (a + b + c) / 2;
+      _ref = box.rowwise().sum() / 2;
 
-      cout << "Refernce is center of box " << _ref << endl;
+      cout << "Reference is center of box " << _ref << endl;
     }
 
-    _outfile.open(_outfilename.c_str());
+    _outfile.open(_outfilename);
     if (!_outfile) {
-      throw runtime_error("cannot open outfile for output");
+      throw runtime_error("cannot open" + _outfilename + " for output");
     }
   }
 
@@ -147,10 +133,9 @@ class CsgFluctuations : public CsgApplication {
  protected:
   // number of particles in dV
   int _nbins;
-  double *_N_avg;
+  Eigen::VectorXd _N_avg;
   // sqare
-  double *_N_sq_avg;
-  int *N;
+  Eigen::VectorXd _N_sq_avg;
   string _filter;
   string _refmol;
   double _rmax;
@@ -170,11 +155,7 @@ int main(int argc, char **argv) {
   return app.Exec(argc, argv);
 }
 
-void CsgFluctuations::EvalConfiguration(Topology *conf,
-                                        Topology *conf_atom = nullptr) {
-  Eigen::Vector3d eR;
-  double r = 0;
-  int rbin;
+void CsgFluctuations::EvalConfiguration(Topology *conf, Topology *) {
 
   if (_refmol != "") {
     for (Bead *bead : conf->Beads()) {
@@ -185,21 +166,20 @@ void CsgFluctuations::EvalConfiguration(Topology *conf,
     }
   }
 
-  for (int i = 0; i < _nbins; i++) {
-    N[i] = 0;
-  }
+  votca::tools::HistogramNew hist;
+  hist.Initialize(_rmin, _rmax, _nbins);
 
   /* check how many molecules are in each bin*/
   for (Bead *bead : conf->Beads()) {
     if (!votca::tools::wildcmp(_filter.c_str(), bead->getName().c_str())) {
       continue;
     }
-
+    double r = 0;
     if (_do_spherical) {
-      eR = bead->getPos() - _ref;
+      Eigen::Vector3d eR = bead->getPos() - _ref;
       r = eR.norm();
     } else {
-      eR = bead->getPos();
+      Eigen::Vector3d eR = bead->getPos();
       if (_dim == 0) {
         r = eR.x();
       } else if (_dim == 1) {
@@ -208,17 +188,12 @@ void CsgFluctuations::EvalConfiguration(Topology *conf,
         r = eR.z();
       }
     }
-    if (r > _rmin && r < _rmax) {
-      rbin = (int)_nbins * (double)((r - _rmin) / (_rmax - _rmin));
-      N[rbin]++;
-    }
+    hist.Process(r);
   }
 
   /* update averages*/
-  for (int i = 0; i < _nbins; i++) {
-    _N_avg[i] += N[i];
-    _N_sq_avg[i] += N[i] * N[i];
-  }
+  _N_avg += hist.data().y();
+  _N_sq_avg += hist.data().y().cwiseAbs2();
 
   _nframes++;
 }

orientcorr/orientcorr.cc

@@ -80,7 +80,6 @@ string OrientCorrApp::_nbmethod;
 class MyWorker : public CsgApplication::Worker {
  public:
   ~MyWorker() override = default;
-  ;
 
   // evaluate the current frame
   void EvalConfiguration(Topology *top, Topology *top_ref) override;
@@ -135,7 +134,7 @@ NBList *OrientCorrApp::CreateNBSearch() {
 }
 
 // initialize the histograms
-void OrientCorrApp::BeginEvaluate(Topology *top, Topology *top_ref) {
+void OrientCorrApp::BeginEvaluate(Topology *, Topology *) {
   _cor.Initialize(0, _cut_off, _nbins);
   _count.Initialize(0, _cut_off, _nbins);
   _cor_excl.Initialize(0, _cut_off, _nbins);
@@ -155,7 +154,7 @@ CsgApplication::Worker *OrientCorrApp::ForkWorker() {
 }
 
 // evaluates a frame
-void MyWorker::EvalConfiguration(Topology *top, Topology *top_ref) {
+void MyWorker::EvalConfiguration(Topology *top, Topology *) {
 
   // first genearate a mapped topology
   // the beads are sitting on the bonds and have an orientation which
@@ -193,8 +192,8 @@ void MyWorker::EvalConfiguration(Topology *top, Topology *top_ref) {
   cout << "done\n";
 
   // the neighbor search only finds pairs, add self-self correlation parts here
-  _cor.Process(0.0f, mapped.BeadCount());
-  _count.Process(0.0f, mapped.BeadCount());
+  _cor.Process(0.0f, (double)mapped.BeadCount());
+  _count.Process(0.0f, (double)mapped.BeadCount());
 
   // search for all beads
   BeadList b;
@@ -215,7 +214,7 @@ void MyWorker::EvalConfiguration(Topology *top, Topology *top_ref) {
 
 // process a pair, since return value is falsed, pairs are not cached which
 // saves a lot of memory for the big systems
-bool MyWorker::FoundPair(Bead *b1, Bead *b2, const Eigen::Vector3d &r,
+bool MyWorker::FoundPair(Bead *b1, Bead *b2, const Eigen::Vector3d &,
                          const double dist) {
   double tmp = b1->getV().dot(b2->getV());
   double P2 = 3. / 2. * tmp * tmp - 0.5;