Merge branch 'python' into fix-3907

CMakeLists.txt

@@ -387,6 +387,8 @@ target_compile_options(
             $<$<BOOL:${WARNINGS_ARE_ERRORS}>:-Werror>
             # add extra warnings
             $<$<CXX_COMPILER_ID:Clang>:-Wextern-initializer>
+            $<$<CXX_COMPILER_ID:Clang>:-Wrange-loop-analysis>
+            -Wfloat-conversion
             # disable warnings from -Wextra
             -Wno-sign-compare
             -Wno-unused-function

doc/sphinx/analysis.rst

@@ -453,8 +453,6 @@ documentation for all available observables in :mod:`espressomd.observables`.
 
 - Observables working on a given set of particles and returning reduced quantities:
 
-   - :class:`~espressomd.observables.Current`: Total current of the system
-
    - :class:`~espressomd.observables.DipoleMoment`: Total electric dipole moment of the system obtained based on unfolded positions
 
    - :class:`~espressomd.observables.MagneticDipoleMoment`: Total magnetic dipole moment of the system based on the :attr:`espressomd.particle_data.ParticleHandle.dip` property.

doc/sphinx/inter_bonded.rst

@@ -87,34 +87,6 @@ The third, optional parameter defines a cutoff radius. Whenever a
 harmonic bond gets longer than :math:`r_\mathrm{cut}`, the bond will be reported as broken,
 and a background error will be raised.
 
-.. _Harmonic Dumbbell Bond:
-
-Harmonic Dumbbell Bond
-~~~~~~~~~~~~~~~~~~~~~~
-
-.. note::
-
-    Requires ``ROTATION`` feature.
-
-
-A harmonic Dumbbell bond can be instantiated via
-:class:`espressomd.interactions.HarmonicDumbbellBond`::
-
-    from espressomd.interactions import HarmonicDumbbellBond
-    hdb = HarmonicDumbbellBond(k1=<float>, k2=<float>, r_0=<float>, r_cut=<float>)
-
-
-This bond is similar to the normal harmonic bond in such a way that it
-sets up a harmonic potential, i.e. a spring, between the two particles.
-Additionally the orientation of the first particle in the bond will be aligned along
-the distance vector between both particles. This alignment can be
-controlled by the second harmonic constant :math:`k_2`. Keep in mind that orientation will
-oscillate around the distance vector and some kind of
-friction needs to be present for it to relax.
-
-The roles of the parameters :math:`k_1, r_0, r_\mathrm{cut}` are exactly the same as for the
-harmonic bond.
-
 .. _Quartic bond:
 
 Quartic bond

src/core/DomainDecomposition.cpp

@@ -285,7 +285,8 @@ void DomainDecomposition::create_cell_grid(double range) {
 
   if (range <= 0.) {
     /* this is the non-interacting case */
-    const int cells_per_dir = std::ceil(std::pow(min_num_cells, 1. / 3.));
+    auto const cells_per_dir =
+        static_cast<int>(std::ceil(std::pow(min_num_cells, 1. / 3.)));
 
     cell_grid[0] = cells_per_dir;
     cell_grid[1] = cells_per_dir;

src/core/actor/DipolarBarnesHut_cuda.cu

@@ -250,7 +250,7 @@ __global__ __launch_bounds__(THREADS2, FACTOR2) void treeBuildingKernel() {
       j = 0;
       for (l = 0; l < 3; l++)
         if (root[l] < p[l])
-          j += pow(2, l);
+          j += static_cast<int>(pow(2, l));
     }
 
     // Follow path to leaf cell. Should not happen at the first iteration of
@@ -283,7 +283,7 @@ __global__ __launch_bounds__(THREADS2, FACTOR2) void treeBuildingKernel() {
       // j=0..7 determines the octant in a binary representations.
       for (l = 0; l < 3; l++)
         if (bhpara->r[3 * n + l] < p[l])
-          j += pow(2, l);
+          j += static_cast<int>(pow(2, l));
       ch = bhpara->child[n * 8 + j];
     }
     // Now we are deep enough in the tree, passed all levels of cells and
@@ -390,7 +390,7 @@ __global__ __launch_bounds__(THREADS2, FACTOR2) void treeBuildingKernel() {
             j = 0;
             for (l = 0; l < 3; l++)
               if (pos[l] < bhpara->r[3 * ch + l])
-                j += pow(2, l);
+                j += static_cast<int>(pow(2, l));
             // New element just appeared in the chain of cells. Hence, that what
             // supposed to be a child ("ch") before entering the present
             // iteration, now will be a child of the new cell (after this
@@ -406,7 +406,7 @@ __global__ __launch_bounds__(THREADS2, FACTOR2) void treeBuildingKernel() {
             // given thread and block against new octant cell (pos[l]):
             for (l = 0; l < 3; l++)
               if (pos[l] < p[l])
-                j += pow(2, l);
+                j += static_cast<int>(pow(2, l));
 
             // Now the current cell's child should be considering in the new
             // particle new octant:

src/core/actor/DipolarDirectSum.hpp

@@ -61,7 +61,7 @@ class DipolarDirectSum : public Actor {
     dds_float box[3];
     int per[3];
     for (int i = 0; i < 3; i++) {
-      box[i] = s.box()[i];
+      box[i] = static_cast<dds_float>(s.box()[i]);
       per[i] = (box_geo.periodic(i));
     }
     DipolarDirectSum_kernel_wrapper_force(
@@ -72,7 +72,7 @@ class DipolarDirectSum : public Actor {
     dds_float box[3];
     int per[3];
     for (int i = 0; i < 3; i++) {
-      box[i] = s.box()[i];
+      box[i] = static_cast<dds_float>(s.box()[i]);
       per[i] = (box_geo.periodic(i));
     }
     DipolarDirectSum_kernel_wrapper_energy(

src/core/bonded_interactions/CMakeLists.txt

@@ -10,7 +10,6 @@ target_sources(
           ${CMAKE_CURRENT_SOURCE_DIR}/dihedral.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/fene.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/harmonic.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/harmonic_dumbbell.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/quartic.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/thermalized_bond.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/umbrella.cpp)

src/core/bonded_interactions/bonded_interaction_data.cpp

@@ -38,8 +38,6 @@ auto cutoff(int type, Bond_parameters const &bp) {
     return bp.fene.cutoff();
   case BONDED_IA_HARMONIC:
     return bp.harmonic.cutoff();
-  case BONDED_IA_HARMONIC_DUMBBELL:
-    return bp.harmonic_dumbbell.cutoff();
   case BONDED_IA_QUARTIC:
     return bp.quartic.cutoff();
   case BONDED_IA_BONDED_COULOMB:

src/core/bonded_interactions/bonded_interaction_data.hpp

@@ -367,7 +367,6 @@ union Bond_parameters {
   Oif_global_forces_bond_parameters oif_global_forces;
   Oif_local_forces_bond_parameters oif_local_forces;
   Harmonic_bond_parameters harmonic;
-  Harmonic_dumbbell_bond_parameters harmonic_dumbbell;
   Quartic_bond_parameters quartic;
   Bonded_coulomb_bond_parameters bonded_coulomb;
   Bonded_coulomb_sr_bond_parameters bonded_coulomb_sr;

src/core/cluster_analysis/ClusterStructure.cpp

@@ -54,7 +54,7 @@ void ClusterStructure::run_for_all_pairs() {
 void ClusterStructure::run_for_bonded_particles() {
   clear();
   for (const auto &p : partCfg()) {
-    for (auto const &bond : p.bonds()) {
+    for (auto const bond : p.bonds()) {
       if (bond.partner_ids().size() == 1) {
         add_pair(p, get_particle_data(bond.partner_ids()[0]));
       }

src/core/energy_inline.hpp

@@ -36,7 +36,6 @@
 #include "bonded_interactions/dihedral.hpp"
 #include "bonded_interactions/fene.hpp"
 #include "bonded_interactions/harmonic.hpp"
-#include "bonded_interactions/harmonic_dumbbell.hpp"
 #include "bonded_interactions/quartic.hpp"
 #include "bonded_interactions/umbrella.hpp"
 #include "errorhandling.hpp"
@@ -219,10 +218,6 @@ calc_bonded_energy(Bonded_ia_parameters const &iaparams, Particle const &p1,
     switch (type) {
     case BONDED_IA_FENE:
       return fene_pair_energy(iaparams, dx);
-#ifdef ROTATION
-    case BONDED_IA_HARMONIC_DUMBBELL:
-      return harmonic_dumbbell_pair_energy(p1.r.calc_director(), iaparams, dx);
-#endif
     case BONDED_IA_HARMONIC:
       return harmonic_pair_energy(iaparams, dx);
     case BONDED_IA_QUARTIC:

src/core/forces_inline.hpp

@@ -30,7 +30,6 @@
 #include "bonded_interactions/dihedral.hpp"
 #include "bonded_interactions/fene.hpp"
 #include "bonded_interactions/harmonic.hpp"
-#include "bonded_interactions/harmonic_dumbbell.hpp"
 #include "bonded_interactions/quartic.hpp"
 #include "bonded_interactions/thermalized_bond.hpp"
 #include "bonded_interactions/umbrella.hpp"
@@ -302,27 +301,14 @@ inline void add_non_bonded_pair_force(Particle &p1, Particle &p2,
  *  @param[in] p2          Second particle.
  *  @param[in] iaparams    Bonded parameters for the interaction.
  *  @param[in] dx          Vector between @p p1 and @p p2.
- *  @param[out] torque     Torque on @p p1.
  */
 inline boost::optional<Utils::Vector3d>
 calc_bond_pair_force(Particle const &p1, Particle const &p2,
                      Bonded_ia_parameters const &iaparams,
-                     Utils::Vector3d const &dx, Utils::Vector3d &torque) {
+                     Utils::Vector3d const &dx) {
   switch (iaparams.type) {
   case BONDED_IA_FENE:
     return fene_pair_force(iaparams, dx);
-#ifdef ROTATION
-  case BONDED_IA_HARMONIC_DUMBBELL: {
-    auto values =
-        harmonic_dumbbell_pair_force(p1.r.calc_director(), iaparams, dx);
-    if (values) {
-      torque = std::get<1>(values.get());
-      return boost::optional<Utils::Vector3d>(std::get<0>(values.get()));
-    }
-
-    return {};
-  }
-#endif
   case BONDED_IA_HARMONIC:
     return harmonic_pair_force(iaparams, dx);
   case BONDED_IA_QUARTIC:
@@ -363,16 +349,11 @@ inline bool add_bonded_two_body_force(Bonded_ia_parameters const &iaparams,
     }
   }
   default: {
-    Utils::Vector3d torque1{};
-    auto result = calc_bond_pair_force(p1, p2, iaparams, dx, torque1);
+    auto result = calc_bond_pair_force(p1, p2, iaparams, dx);
     if (result) {
       p1.f.f += result.get();
       p2.f.f -= result.get();
 
-#ifdef ROTATION
-      p1.f.torque += torque1;
-#endif
-
 #ifdef NPT
       npt_add_virial_contribution(result.get(), dx);
 #endif

src/core/grid.cpp

@@ -52,7 +52,7 @@ int map_position_node_array(const Utils::Vector3d &pos) {
 
   Utils::Vector3i im;
   for (int i = 0; i < 3; i++) {
-    im[i] = std::floor(f_pos[i] / local_geo.length()[i]);
+    im[i] = static_cast<int>(std::floor(f_pos[i] / local_geo.length()[i]));
     im[i] = boost::algorithm::clamp(im[i], 0, node_grid[i] - 1);
   }