OpenMP test branch

.gitattributes

@@ -1,2 +1,5 @@
 *.ipynb filter=nbstripout
 *.ipynb diff=ipynb
+
+examples/zundel_i-PI.ipynb filter= diff=
+

CMakeLists.txt

@@ -81,7 +81,7 @@ SET(TYPE_ARCHITECTURE "native" CACHE STRING
 )
 
 ########## COMPILATION FLAGS ##########
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Weffc++ -Wno-non-virtual-dtor")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Weffc++ -Wno-non-virtual-dtor -fopenmp")
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -Wextra")
 
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" OR

src/rascal/models/sparse_kernel_predict.hh

@@ -127,6 +127,8 @@ namespace rascal {
 
     math::Vector_t weights_scaled(weights.size());
     size_t i_row{0};
+
+#pragma omp for
     for (auto center : manager) {
       const int a_sp{center.get_atom_type()};
       // compute contraction of the model weights with the gradient of the

src/rascal/models/sparse_kernels.hh

@@ -178,6 +178,7 @@ namespace rascal {
         for (auto & manager : managers) {
           auto && propA{*manager->template get_property<Property_t>(
               representation_name, true)};
+#pragma omp for              
           for (auto center : manager) {
             int sp = center.get_atom_type();
             KNM.row(ii_A) =
@@ -321,6 +322,7 @@ namespace rascal {
           if (zeta > 1) {
             dkdX_missing_T.setZero();
             // zeta * (X * T)**(zeta-1)
+#pragma omp for            
             for (auto center : manager) {
               int a_species{center.get_atom_type()};
               dkdX_missing_T[center] =
@@ -362,6 +364,7 @@ namespace rascal {
           if (do_block_by_key_dot) {
             size_t idx_row{0};
             auto repr_grads = prop_repr_grad.get_raw_data_view();
+#pragma omp for            
             for (auto center : manager) {
               int a_species{center.get_atom_type()};
               Eigen::Vector3d r_i = center.get_position();
@@ -447,6 +450,7 @@ namespace rascal {
               idx_row += nb_rows;
             }  // center
           } else {
+#pragma omp for              
             for (auto center : manager) {
               int a_species{center.get_atom_type()};
               Eigen::Vector3d r_i = center.get_position();

src/rascal/representations/calculator_spherical_expansion.hh

@@ -1791,6 +1791,7 @@ namespace rascal {
     // coeff C^{ij}_{nlm}
     auto c_ij_nlm = math::Matrix_t(n_row, n_col);
 
+#pragma omp for
     for (auto center : manager) {
       // c^{i}
       auto & coefficients_center = expansions_coefficients[center];

src/rascal/representations/calculator_spherical_invariants.hh

@@ -605,6 +605,7 @@ namespace rascal {
       Eigen::Vector3d soap_vector_dot_gradient{};
 
       // compute the dot product and update the gradients to be normalized
+#pragma omp for      
       for (auto center : manager) {
         for (auto neigh : center.pairs_with_self_pair()) {
           const auto & soap_vector = soap_vectors[center];
@@ -744,6 +745,7 @@ namespace rascal {
         *manager, "power spectrums inverse norms", true};
     soap_vector_norm_inv.resize();
 
+#pragma omp for
     for (auto center : manager) {
       auto & coefficients{expansions_coefficients[center]};
       auto & soap_vector{soap_vectors[center]};
@@ -976,6 +978,7 @@ namespace rascal {
         *manager, "radial spectrum inverse norms", ExcludeGhosts};
     soap_vector_norm_inv.resize();
 
+#pragma omp for
     for (auto center : manager) {
       const auto & coefficients{expansions_coefficients[center]};
       auto & soap_vector{soap_vectors[center]};
@@ -1048,7 +1051,12 @@ namespace rascal {
     double mult{1.0};
     Key_t trip_type{0, 0, 0};
     internal::SortedKey<Key_t> triplet_type{trip_type};
-    for (auto center : manager) {
+
+#pragma omp for    
+    for (auto iter = manager->begin(); iter<manager->end(); ++iter) {
+      std::cerr<<"computing "<<iter.get_index()<< " out of "<<   manager->end().get_index()<<"\n";
+      auto center = *iter;
+//    for (auto center : manager) {  
       auto & coefficients{expansions_coefficients[center]};
       auto & soap_vector{soap_vectors[center]};
 

src/rascal/structure_managers/structure_manager.hh

@@ -1387,6 +1387,20 @@ namespace rascal {
       return *this;
     }
 
+    //! int increment
+    Iterator & operator+=(size_t increment) {
+      this->index += increment;
+      return *this;
+    }
+
+    //! int decrement
+    Iterator & operator-=(size_t increment) {
+      this->index -= increment;
+      return *this;
+    }
+    //! subtraction between iterators
+    auto operator-(const Iterator & other) { return this->index - other.index; }
+
     value_type operator*() {
       auto & cluster_indices_properties = std::get<Order - 1>(
           this->get_manager().get_cluster_indices_container());
@@ -1420,6 +1434,22 @@ namespace rascal {
       return not(*this == other);
     }
 
+    //! comparison operators
+    bool operator<(const Iterator & other) { return this->index < other.index; }
+
+    bool operator>(const Iterator & other) { return this->index > other.index; }
+
+    bool operator<=(const Iterator & other) {
+      return this->index <= other.index;
+    }
+
+    bool operator>=(const Iterator & other) {
+      return this->index >= other.index;
+    }
+
+    size_t get_index() {
+        return this->index;
+    }
     /**
      * const access to container
      */