Merge branch 'python' of https://github.com/espressomd/espresso into …

…lb_test

doc/doxygen/Doxyfile

@@ -1472,13 +1472,13 @@ ENABLE_PREPROCESSING   = YES
 # compilation will be performed. Macro expansion can be done in a controlled
 # way by setting EXPAND_ONLY_PREDEF to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
 # then the macro expansion is limited to the macros specified with the
 # PREDEFINED and EXPAND_AS_DEFINED tags.
 
-EXPAND_ONLY_PREDEF     = NO
+EXPAND_ONLY_PREDEF     = YES
 
 # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
 # pointed to by INCLUDE_PATH will be searched when a #include is found.
@@ -1515,7 +1515,8 @@ INCLUDE_FILE_PATTERNS  = *.h *.hpp *.cuh
 # Use the PREDEFINED tag if you want to use a different macro definition that
 # overrules the definition found in the source code.
 
-EXPAND_AS_DEFINED      =
+EXPAND_AS_DEFINED      = NEW_CYLINDRICAL_PROFILE_OBSERVABLE \
+                         NEW_PARAMLESS_OBSERVABLE
 
 # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
 # doxygen's preprocessor will remove all references to function-like macros

doc/doxygen/gen_doxyconfig.py

@@ -61,7 +61,7 @@
 
 for feature in sorted(defs.allfeatures):
     configfile.write("  {} \\\n".format(feature))
-configfile.write("  DOXYGEN \\\n".format(feature))
+configfile.write("  DOXYGEN\n".format(feature))
 
 configfile.close()
 print("Done.")

src/core/MpiCallbacks.hpp

@@ -68,10 +68,10 @@ struct callback_concept_t {
 };
 
 /**
- * @brief Concrete implementation of @class callback_concept_t.
+ * @brief Concrete implementation of @ref callback_concept_t.
  *
  * This is an implementation of a callback for a specific callable
- * F and a set of arguments to call it with.
+ * @p F and a set of arguments to call it with.
  */
 template <class F, class... Args>
 struct callback_model_t final : public callback_concept_t {
@@ -129,7 +129,7 @@ auto make_model_impl(CRef &&c, FunctorTypes<C, R, Args...>) {
 }
 
 /**
- * @brief Make a @class callback_model_t for a functor or lambda.
+ * @brief Make a @ref callback_model_t for a functor or lambda.
  *
  * The signature is deduced from F::operator() const, which has
  * to exist and can not be overloaded.
@@ -139,7 +139,7 @@ template <typename F> auto make_model(F &&f) {
 }
 
 /**
- * @brief Make a @class callback_model_t for a function pointer.
+ * @brief Make a @ref callback_model_t for a function pointer.
  *
  * This instantiates a implementation of a callback for a function
  * pointer. The main task here is to transfer the signature from
@@ -319,8 +319,7 @@ class MpiCallbacks {
    * in the MPI loop.
    *
    * @param id The callback to call.
-   * @param par1 First parameter to pass to the callback.
-   * @param par2 Second parameter to pass to the callback.
+   * @param args Arguments for the callback.
    */
   template <class... Args> void call(int id, Args &&... args) const {
     /** Can only be call from master */
@@ -352,7 +351,7 @@ class MpiCallbacks {
    * The method can only be called the master
    * and has the prerequisite that the other nodes are
    * in the MPI loop. Also the function has to be previously
-   * registered e.g. with the @def REGISTER_CALLBACK macro.
+   * registered e.g. with the @ref REGISTER_CALLBACK macro.
    *
    * @param fp Pointer to the function to call.
    * @param args Arguments for the callback.
@@ -446,7 +445,7 @@ using CallbackHandle = MpiCallbacks::CallbackHandle<Args...>;
 /**
  * @brief Helper class to atomatically add callbacks.
  *
- * Should not be used directly, but via @def REGISTER_CALLBACK.
+ * Should not be used directly, but via @ref REGISTER_CALLBACK.
  */
 class RegisterCallback {
 

src/core/communication.hpp

@@ -327,14 +327,4 @@ std::vector<int> mpi_resort_particles(int global_flag);
 
 /*@}*/
 
-/** \name Event codes for \ref mpi_bcast_event
- *  These codes are used by \ref mpi_bcast_event to notify certain changes
- *  of doing something now.
- */
-/*@{*/
-#define P3M_COUNT_CHARGES 0
-#define CHECK_PARTICLES 2
-#define P3M_COUNT_DIPOLES 5
-/*@}*/
-
 #endif

src/core/debug.hpp

@@ -35,8 +35,7 @@
  */
 void check_particle_consistency();
 
-/** check the consistency of the cells and particle_node. Called from
- *  mpi_bcast_event(CHECK_PARTICLES)
+/** check the consistency of the cells and particle_node.
  */
 void check_particles();
 

src/core/event.hpp

@@ -96,8 +96,8 @@ void on_temperature_change();
 
 /** called every time other parameters (timestep,...) are changed. Note that
  *  this does not happen automatically. The callback procedure of the changed
- *  variable is responsible for that by calling \ref mpi_bcast_event (2).
- *  @param parameter is the FIELD_* identifier of the field changed.
+ *  variable is responsible for that.
+ *  @param parameter is the @ref Fields identifier of the field changed.
  */
 void on_parameter_change(int parameter);
 

src/core/forces_inline.hpp

@@ -509,24 +509,19 @@ inline int calc_bond_pair_force(Particle *p1, Particle *p2,
  */
 inline void add_bonded_force(Particle *p1) {
   Particle *p3 = nullptr, *p4 = nullptr;
-  Bonded_ia_parameters *iaparams;
-  int i, j, bond_broken = 1;
+  int bond_broken = 1;
 
-  i = 0;
+  int i = 0;
   while (i < p1->bl.n) {
     double dx[3] = {0., 0., 0.};
     double force[3] = {0., 0., 0.};
     double force2[3] = {0., 0., 0.};
     double force3[3] = {0., 0., 0.};
 #if defined(OIF_LOCAL_FORCES)
     double force4[3] = {0., 0., 0.};
-#endif
-#ifdef ROTATION
-    double torque1[3] = {0., 0., 0.};
-    double torque2[3] = {0., 0., 0.};
 #endif
     int type_num = p1->bl.e[i++];
-    iaparams = &bonded_ia_params[type_num];
+    auto iaparams = &bonded_ia_params[type_num];
     int type = iaparams->type;
     int n_partners = iaparams->num;
 
@@ -616,11 +611,6 @@ inline void add_bonded_force(Particle *p1) {
 #ifdef IMMERSED_BOUNDARY
       case BONDED_IA_IBM_TRIEL:
         bond_broken = IBM_Triel_CalcForce(p1, p2, p3, iaparams);
-        // These may be added later on, but we set them to zero because the
-        // force has already been added in IBM_Triel_CalcForce
-        force[0] = force2[0] = force3[0] = 0;
-        force[1] = force2[1] = force3[1] = 0;
-        force[2] = force2[2] = force3[2] = 0;
         break;
 #endif
       default:
@@ -646,29 +636,9 @@ inline void add_bonded_force(Particle *p1) {
 // IMMERSED_BOUNDARY
 #ifdef IMMERSED_BOUNDARY
       case BONDED_IA_IBM_TRIBEND: {
-        // First build neighbor list. This includes all nodes around the central
-        // node.
-        const int numNeighbors = iaparams->num;
-        auto **neighbors = new Particle *[numNeighbors];
-        // Three are already there
-        neighbors[0] = p2;
-        neighbors[1] = p3;
-        neighbors[2] = p4;
-        // Get rest
-        for (int j = 3; j < numNeighbors; j++)
-          neighbors[j] = local_particles[p1->bl.e[i++]];
-
-        IBM_Tribend_CalcForce(p1, numNeighbors, neighbors, *iaparams);
+        IBM_Tribend_CalcForce(p1, p2, p3, p4, *iaparams);
         bond_broken = 0;
 
-        // Clean up
-        delete[] neighbors;
-
-        // These may be added later on, but we set them to zero because the
-        // force has
-        force[0] = force2[0] = force3[0] = 0;
-        force[1] = force2[1] = force3[1] = 0;
-        force[2] = force2[2] = force3[2] = 0;
         break;
       }
 #endif
@@ -701,7 +671,7 @@ inline void add_bonded_force(Particle *p1) {
         continue;
       }
 
-      for (j = 0; j < 3; j++) {
+      for (int j = 0; j < 3; j++) {
         switch (type) {
         case BONDED_IA_THERMALIZED_DIST:
           p1->f.f[j] += force[j];
@@ -710,10 +680,6 @@ inline void add_bonded_force(Particle *p1) {
         default:
           p1->f.f[j] += force[j];
           p2->f.f[j] -= force[j];
-#ifdef ROTATION
-          p1->f.torque[j] += torque1[j];
-          p2->f.torque[j] += torque2[j];
-#endif
         }
       }
       break;
@@ -725,7 +691,7 @@ inline void add_bonded_force(Particle *p1) {
         continue;
       }
 
-      for (j = 0; j < 3; j++) {
+      for (int j = 0; j < 3; j++) {
         switch (type) {
         default:
           p1->f.f[j] += force[j];
@@ -744,7 +710,7 @@ inline void add_bonded_force(Particle *p1) {
 
       switch (type) {
       case BONDED_IA_DIHEDRAL:
-        for (j = 0; j < 3; j++) {
+        for (int j = 0; j < 3; j++) {
           p1->f.f[j] += force[j];
           p2->f.f[j] += force2[j];
           p3->f.f[j] += force3[j];
@@ -754,7 +720,7 @@ inline void add_bonded_force(Particle *p1) {
 
 #ifdef OIF_LOCAL_FORCES
       case BONDED_IA_OIF_LOCAL_FORCES:
-        for (j = 0; j < 3; j++) {
+        for (int j = 0; j < 3; j++) {
           p1->f.f[j] += force2[j];
           p2->f.f[j] += force[j];
           p3->f.f[j] += force3[j];

src/core/immersed_boundary/ibm_tribend.cpp

@@ -27,36 +27,18 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "immersed_boundary/ibm_tribend.hpp"
 #include "particle_data.hpp"
 
-// DEBUG
-/*double maxBendingForce;
-double maxBendingDist;
-double maxX;*/
-
 /*************
    IBM_Tribend_CalcForce
 Calculate the bending force and add it to the particles
  **************/
 
-void IBM_Tribend_CalcForce(Particle *p1, const int numPartners,
-                           Particle **const partners,
-                           const Bonded_ia_parameters &iaparams) {
-  // move to separate function
-  if (numPartners != 3) {
-    throw std::runtime_error("IBM_Tribend expects 3 bond partners.");
-  }
-
-  Particle *p2 = partners[0];
-  Particle *p3 = partners[1];
-  Particle *p4 = partners[2];
-
+void IBM_Tribend_CalcForce(Particle *p1, Particle *p2, Particle *p3,
+                           Particle *p4, const Bonded_ia_parameters &iaparams) {
   assert(p1);
   assert(p2);
   assert(p3);
   assert(p4);
 
-  // ************* This is Wolfgang's code **************
-  // with some corrections by Achim
-
   // Get vectors making up the two triangles
   double dx1[3], dx2[3], dx3[3];
   get_mi_vector(dx1, p1->r.p, p3->r.p);

src/core/immersed_boundary/ibm_tribend.hpp

@@ -26,9 +26,6 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 #include "bonded_interactions/bonded_interaction_data.hpp"
 
-// DEBUG stuff
-extern double maxBendingForce, maxBendingDist, maxX;
-
 // This function is used to set the parameters
 // Also calculates and stores the reference state
 int IBM_Tribend_SetParams(const int bond_type, const int ind1, const int ind2,
@@ -41,9 +38,8 @@ int IBM_Tribend_SetParams(const int bond_type, const int ind1, const int ind2,
 int IBM_Tribend_ResetParams(const int bond_type, const double kb);
 
 // This function calculates and adds the actual force
-void IBM_Tribend_CalcForce(Particle *p1, const int numPartners,
-                           Particle **const partners,
-                           const Bonded_ia_parameters &iaparams);
+void IBM_Tribend_CalcForce(Particle *p1, Particle *p2, Particle *p3,
+                           Particle *p4, const Bonded_ia_parameters &iaparams);
 
 #endif
 

src/core/unit_tests/AS_erfc_part_test.cpp

@@ -24,6 +24,9 @@ using Utils::AS_erfc_part;
 
 #include <cmath>
 
+/* Check that it can be used in constexpr context */
+static_assert((AS_erfc_part(0.), true), "");
+
 BOOST_AUTO_TEST_CASE(approx) {
   for (double x = 0.0; x <= 1.; x += 0.01) {
     auto const approx = AS_erfc_part(x);

src/core/unit_tests/int_pow_test.cpp

@@ -24,12 +24,20 @@
 #include <boost/test/unit_test.hpp>
 
 #include "utils/math/int_pow.hpp"
+#include "utils/math/sqr.hpp"
 using Utils::int_pow;
+using Utils::sqr;
 
 #include <limits>
 
 auto const eps = std::numeric_limits<double>::epsilon();
 
+/* Check that it can be used in constexpr context */
+static_assert((int_pow<11>(2.), true), "");
+
+/* Check that it can be used in constexpr context */
+static_assert((sqr(2.), true), "");
+
 BOOST_AUTO_TEST_CASE(even) {
   const double x = 3.14159;
 
@@ -45,3 +53,7 @@ BOOST_AUTO_TEST_CASE(odd) {
   BOOST_CHECK_CLOSE((x * x) * x, int_pow<3>(x), eps);
   BOOST_CHECK_CLOSE((x * x) * (x * x) * x, int_pow<5>(x), 100. * eps);
 }
+
+BOOST_AUTO_TEST_CASE(square) {
+  BOOST_CHECK_EQUAL(int_pow<2>(3.1415), sqr(3.1415));
+}

src/core/unit_tests/sgn_test.cpp

@@ -26,6 +26,9 @@
 #include "utils/math/sgn.hpp"
 using Utils::sgn;
 
+/* Check that it can be used in constexpr context */
+static_assert(sgn(1), "");
+
 BOOST_AUTO_TEST_CASE(pos) { BOOST_CHECK(1 == sgn(89)); }
 BOOST_AUTO_TEST_CASE(nul) { BOOST_CHECK(0 == sgn(0)); }
 BOOST_AUTO_TEST_CASE(neg) { BOOST_CHECK(-1 == sgn(-89)); }

src/core/utils/Array.hpp

@@ -1,15 +1,11 @@
 #ifndef UTILS_ARRAY_HPP
 #define UTILS_ARRAY_HPP
 
+#include "device_qualifier.hpp"
+
 #include <boost/serialization/access.hpp>
 #include <cstddef>
 
-#if defined(__CUDACC__)
-#define DEVICE_QUALIFIER __host__ __device__
-#else
-#define DEVICE_QUALIFIER
-#endif
-
 namespace Utils {
 
 namespace detail {
@@ -135,5 +131,4 @@ template <typename T, std::size_t N> struct Array {
 };
 
 } // namespace Utils
-#undef DEVICE_QUALIFIER
 #endif