dxmin checking bug + error on nonexistent species

src/framework/domain/metadomain.cpp

@@ -369,6 +369,8 @@ namespace ntt {
 
   template <SimEngine::type S, class M>
   void Metadomain<S, M>::metricCompatibilityCheck() const {
+    const auto epsilon = std::numeric_limits<real_t>::epsilon() *
+                         static_cast<real_t>(100.0);
     const auto dx_min              = g_mesh.metric.dxMin();
     auto       dx_min_from_domains = std::numeric_limits<real_t>::infinity();
     for (unsigned int idx { 0 }; idx < g_ndomains; ++idx) {
@@ -377,7 +379,7 @@ namespace ntt {
       dx_min_from_domains = std::min(dx_min_from_domains, current_dx_min);
     }
     raise::ErrorIf(
-      not cmp::AlmostEqual(dx_min, dx_min_from_domains),
+      not cmp::AlmostEqual(dx_min / dx_min_from_domains, ONE, epsilon),
       "dx_min is not the same across all domains: " + std::to_string(dx_min) +
         " " + std::to_string(dx_min_from_domains),
       HERE);

src/framework/domain/output.cpp

@@ -125,6 +125,11 @@ namespace ntt {
         }
       }
     }
+    for (const auto& sp : specs) {
+      raise::ErrorIf((sp > prtl_species.size()) or (sp == 0),
+                     "Invalid species index " + std::to_string(sp),
+                     HERE);
+    }
     auto scatter_buff = Kokkos::Experimental::create_scatter_view(buffer);
 
     // some parameters

src/framework/tests/comm_mpi.cpp

@@ -58,4 +58,4 @@ auto main(int argc, char* argv[]) -> int {
 
   Kokkos::finalize();
   return 0;
-}
+}

src/output/tests/writer-mpi.cpp

@@ -60,7 +60,7 @@ auto main(int argc, char* argv[]) -> int {
     {
       // write
       auto writer = out::Writer();
-      writer.init(&adios, "hdf5", "test");
+      writer.init(&adios, "hdf5", "test", false);
       writer.defineMeshLayout({ static_cast<unsigned long>(mpi_size) * nx1 },
                               { static_cast<unsigned long>(mpi_rank) * nx1 },
                               { nx1 },
@@ -74,13 +74,13 @@ auto main(int argc, char* argv[]) -> int {
         field_names.push_back(writer.fieldWriters()[0].name(i));
         addresses.push_back(i);
       }
-      writer.beginWriting(0, 0.0);
+      writer.beginWriting(WriteMode::Fields, 0, 0.0);
       writer.writeField<Dim::_1D, 3>(field_names, field, addresses);
-      writer.endWriting();
+      writer.endWriting(WriteMode::Fields);
 
-      writer.beginWriting(1, 0.1);
+      writer.beginWriting(WriteMode::Fields, 1, 0.1);
       writer.writeField<Dim::_1D, 3>(field_names, field, addresses);
-      writer.endWriting();
+      writer.endWriting(WriteMode::Fields);
       adios.ExitComputationBlock();
     }