Merge branch 'bartgol/eamxx/encapsulate-diagnostics-creation' (PR #6796)

Extract creation of diagnostic classes out of the AtmosphereOutput class and into its own routine.

components/eamxx/src/diagnostics/CMakeLists.txt

@@ -1,11 +1,15 @@
 set(DIAGNOSTIC_SRCS
+  aerocom_cld.cpp
+  aodvis.cpp
+  atm_backtend.cpp
   atm_density.cpp
   dry_static_energy.cpp
   exner.cpp
   field_at_height.cpp
   field_at_level.cpp
   field_at_pressure_level.cpp
   longwave_cloud_forcing.cpp
+  number_path.cpp
   potential_temperature.cpp
   precip_surf_mass_flux.cpp
   relative_humidity.cpp
@@ -17,15 +21,11 @@ set(DIAGNOSTIC_SRCS
   virtual_temperature.cpp
   water_path.cpp
   wind_speed.cpp
-  aodvis.cpp
-  number_path.cpp
-  aerocom_cld.cpp
-  atm_backtend.cpp
 )
 
 add_library(diagnostics ${DIAGNOSTIC_SRCS})
 target_link_libraries(diagnostics PUBLIC scream_share)
 
-if (NOT SCREAM_LIB_ONLY)
+if (NOT SCREAM_LIB_ONLY AND NOT SCREAM_ONLY_GENERATE_BASELINES)
   add_subdirectory(tests)
 endif()

components/eamxx/src/diagnostics/aerocom_cld.cpp

@@ -22,8 +22,6 @@ AeroComCld::AeroComCld(const ekat::Comm &comm,
                    "to be 'Bot' or 'Top' in its input parameters.\n");
 }
 
-std::string AeroComCld::name() const { return "AeroComCld" + m_topbot; }
-
 void AeroComCld::set_grids(
     const std::shared_ptr<const GridsManager> grids_manager) {
   using namespace ekat::units;
@@ -76,7 +74,8 @@ void AeroComCld::set_grids(
   m_dz.allocate_view();
 
   // Construct and allocate the output field
-  FieldIdentifier fid(name(), vector1d_layout, nondim, grid_name);
+
+  FieldIdentifier fid("AeroComCld"+m_topbot, vector1d_layout, nondim, grid_name);
   m_diagnostic_output = Field(fid);
   m_diagnostic_output.allocate_view();
 

components/eamxx/src/diagnostics/aerocom_cld.hpp

@@ -15,7 +15,7 @@ class AeroComCld : public AtmosphereDiagnostic {
   AeroComCld(const ekat::Comm &comm, const ekat::ParameterList &params);
 
   // The name of the diagnostic
-  std::string name() const override;
+  std::string name() const override { return "AeroComCld"; }
 
   // Set the grid
   void set_grids(

components/eamxx/src/diagnostics/field_at_height.cpp

@@ -45,21 +45,16 @@ FieldAtHeight (const ekat::Comm& comm, const ekat::ParameterList& params)
       " - surface reference: " + surf_ref + "\n"
       " -     valid options: sealevel, surface\n");
   m_z_name = (surf_ref == "sealevel") ? "z" : "height";
-  const auto& location = m_params.get<std::string>("vertical_location");
-  auto chars_start = location.find_first_not_of("0123456789.");
-  EKAT_REQUIRE_MSG (chars_start!=0 && chars_start!=std::string::npos,
-      "Error! Invalid string for height value for FieldAtHeight.\n"
-      " - input string   : " + location + "\n"
-      " - expected format: Nm, with N integer\n");
-  const auto z_str = location.substr(0,chars_start);
-  m_z = std::stod(z_str);
-
-  const auto units = location.substr(chars_start);
+
+  const auto units = m_params.get<std::string>("height_units");
   EKAT_REQUIRE_MSG (units=="m",
-      "Error! Invalid string for height value for FieldAtHeight.\n"
-      " - input string   : " + location + "\n"
-      " - expected format: Nm, with N integer\n");
-  m_diag_name = m_field_name + "_at_" + m_params.get<std::string>("vertical_location") + "_above_" + surf_ref;
+      "Error! Invalid units for FieldAtHeight.\n"
+      " - input units: " + units + "\n"
+      " - valid units: m\n");
+
+  auto z_val = m_params.get<std::string>("height_value");
+  m_z = std::stod(z_val);
+  m_diag_name = m_field_name + "_at_" + z_val + units + "_above_" + surf_ref;
 }
 
 void FieldAtHeight::

components/eamxx/src/diagnostics/field_at_height.hpp

@@ -18,7 +18,7 @@ class FieldAtHeight : public AtmosphereDiagnostic
   FieldAtHeight (const ekat::Comm& comm, const ekat::ParameterList& params);
 
   // The name of the diagnostic
-  std::string name () const { return m_diag_name; }
+  std::string name () const { return "FieldAtHeight"; }
 
   // Set the grid
   void set_grids (const std::shared_ptr<const GridsManager> grids_manager);

components/eamxx/src/diagnostics/field_at_level.hpp

@@ -21,7 +21,7 @@ class FieldAtLevel : public AtmosphereDiagnostic
   FieldAtLevel (const ekat::Comm& comm, const ekat::ParameterList& params);
 
   // The name of the diagnostic
-  std::string name () const { return m_diag_name; }
+  std::string name () const { return "FieldAtLevel"; }
 
   // Set the grid
   void set_grids (const std::shared_ptr<const GridsManager> grids_manager);

components/eamxx/src/diagnostics/field_at_pressure_level.cpp

@@ -15,30 +15,22 @@ FieldAtPressureLevel (const ekat::Comm& comm, const ekat::ParameterList& params)
 {
   m_field_name = m_params.get<std::string>("field_name");
 
-  // Figure out the pressure value
-  const auto& location = m_params.get<std::string>("vertical_location");
-  auto chars_start = location.find_first_not_of("0123456789.");
-  EKAT_REQUIRE_MSG (chars_start!=0 && chars_start!=std::string::npos,
-      "Error! Invalid string for pressure value for FieldAtPressureLevel.\n"
-      " - input string   : " + location + "\n"
-      " - expected format: Nxyz, with N integer, and xyz='mb', 'hPa', or 'Pa'\n");
-  const auto press_str = location.substr(0,chars_start);
-  m_pressure_level = std::stod(press_str);
-
-  const auto units = location.substr(chars_start);
+  const auto units = m_params.get<std::string>("pressure_units");
   EKAT_REQUIRE_MSG (units=="mb" or units=="hPa" or units=="Pa",
-      "Error! Invalid string for pressure value for FieldAtPressureLevel.\n"
-      " - input string   : " + location + "\n"
-      " - expected format: Nxyz, with N integer, and xyz='mb', 'hPa', or 'Pa'\n");
+      "Error! Invalid units for FieldAtPressureLevel.\n"
+      " - input units: " + units + "\n"
+      " - valid units: 'mb', 'hPa', 'Pa'\n");
+
+  // Figure out the pressure value, and convert to Pa if needed
+  auto p_value = m_params.get<std::string>("pressure_value");
 
-  // Convert pressure level to Pa, the units of pressure in the simulation
   if (units=="mb" || units=="hPa") {
-    m_pressure_level *= 100;
+    m_pressure_level = std::stod(p_value)*100;
+  } else {
+    m_pressure_level = std::stod(p_value);
   }
 
-  m_mask_val = m_params.get<double>("mask_value",Real(constants::DefaultFillValue<float>::value));
-
-  m_diag_name = m_field_name + "_at_" + location;
+  m_diag_name = m_field_name + "_at_" + p_value + units;
 }
 
 void FieldAtPressureLevel::
@@ -91,6 +83,8 @@ initialize_impl (const RunType /*run_type*/)
   // Add a field representing the mask as extra data to the diagnostic field.
   auto nondim = ekat::units::Units::nondimensional();
   const auto& gname = fid.get_grid_name();
+  m_mask_val = m_params.get<double>("mask_value",Real(constants::DefaultFillValue<float>::value));
+
 
   std::string mask_name = name() + " mask";
   FieldLayout mask_layout( {COL}, {num_cols});

components/eamxx/src/diagnostics/field_at_pressure_level.hpp

@@ -20,7 +20,7 @@ class FieldAtPressureLevel : public AtmosphereDiagnostic
   FieldAtPressureLevel (const ekat::Comm& comm, const ekat::ParameterList& params);
 
   // The name of the diagnostic
-  std::string name () const { return m_diag_name; }
+  std::string name () const { return "FieldAtPressureLevel"; }
 
   // Set the grid
   void set_grids (const std::shared_ptr<const GridsManager> grids_manager);

components/eamxx/src/diagnostics/number_path.cpp

@@ -33,8 +33,6 @@ NumberPathDiagnostic::NumberPathDiagnostic(const ekat::Comm &comm,
   }
 }
 
-std::string NumberPathDiagnostic::name() const { return m_kind + "NumberPath"; }
-
 void NumberPathDiagnostic::set_grids(
     const std::shared_ptr<const GridsManager> grids_manager) {
   using namespace ekat::units;
@@ -55,7 +53,7 @@ void NumberPathDiagnostic::set_grids(
   add_field<Required>(m_nname, scalar3d, 1 / kg, grid_name);
 
   // Construct and allocate the diagnostic field
-  FieldIdentifier fid(name(), scalar2d, kg/(kg*m2), grid_name);
+  FieldIdentifier fid(m_kind + "NumberPath", scalar2d, kg/(kg*m2), grid_name);
   m_diagnostic_output = Field(fid);
   m_diagnostic_output.allocate_view();
 }

components/eamxx/src/diagnostics/number_path.hpp

@@ -16,7 +16,7 @@ class NumberPathDiagnostic : public AtmosphereDiagnostic {
                        const ekat::ParameterList &params);
 
   // The name of the diagnostic
-  std::string name() const;
+  std::string name() const override { return "NumberPath"; }
 
   // Set the grid
   void set_grids(const std::shared_ptr<const GridsManager> grids_manager);

components/eamxx/src/diagnostics/potential_temperature.cpp

@@ -24,11 +24,6 @@ PotentialTemperatureDiagnostic::PotentialTemperatureDiagnostic (const ekat::Comm
   }
 }
 
-std::string PotentialTemperatureDiagnostic::name() const
-{
-  return m_ptype;
-}
-
 // =========================================================================================
 void PotentialTemperatureDiagnostic::set_grids(const std::shared_ptr<const GridsManager> grids_manager)
 {
@@ -51,7 +46,7 @@ void PotentialTemperatureDiagnostic::set_grids(const std::shared_ptr<const Grids
   add_field<Required>("qc",             scalar3d_layout_mid, kg/kg,  grid_name, ps);
 
   // Construct and allocate the diagnostic field
-  FieldIdentifier fid (name(), scalar3d_layout_mid, K, grid_name);
+  FieldIdentifier fid (m_ptype, scalar3d_layout_mid, K, grid_name);
   m_diagnostic_output = Field(fid);
   auto& C_ap = m_diagnostic_output.get_header().get_alloc_properties();
   C_ap.request_allocation(ps);

components/eamxx/src/diagnostics/potential_temperature.hpp

@@ -22,7 +22,7 @@ class PotentialTemperatureDiagnostic : public AtmosphereDiagnostic
   PotentialTemperatureDiagnostic (const ekat::Comm& comm, const ekat::ParameterList& params);
 
   // The name of the diagnostic
-  std::string name () const;
+  std::string name () const override { return "PotentialTemperature"; }
 
   // Set the grid
   void set_grids (const std::shared_ptr<const GridsManager> grids_manager);

components/eamxx/src/diagnostics/precip_surf_mass_flux.cpp

@@ -47,7 +47,7 @@ set_grids(const std::shared_ptr<const GridsManager> grids_manager)
   }
 
   // Construct and allocate the diagnostic field
-  FieldIdentifier fid(name(), scalar2d_layout_mid, m/s, grid_name);
+  FieldIdentifier fid(m_name, scalar2d_layout_mid, m/s, grid_name);
   m_diagnostic_output = Field(fid);
   m_diagnostic_output.get_header().get_alloc_properties().request_allocation();
   m_diagnostic_output.allocate_view();

components/eamxx/src/diagnostics/precip_surf_mass_flux.hpp

@@ -17,7 +17,7 @@ class PrecipSurfMassFlux : public AtmosphereDiagnostic
   PrecipSurfMassFlux (const ekat::Comm& comm, const ekat::ParameterList& params);
 
   // The name of the diagnostic
-  std::string name () const { return m_name; }
+  std::string name () const { return "PrecipSurfMassFlux"; }
 
   // Set the grid
   void set_grids (const std::shared_ptr<const GridsManager> grids_manager);

components/eamxx/src/diagnostics/register_diagnostics.hpp

@@ -36,20 +36,14 @@ inline void register_diagnostics () {
   diag_factory.register_product("AtmosphereDensity",&create_atmosphere_diagnostic<AtmDensityDiagnostic>);
   diag_factory.register_product("Exner",&create_atmosphere_diagnostic<ExnerDiagnostic>);
   diag_factory.register_product("VirtualTemperature",&create_atmosphere_diagnostic<VirtualTemperatureDiagnostic>);
-  diag_factory.register_product("z_int",&create_atmosphere_diagnostic<VerticalLayerDiagnostic>);
-  diag_factory.register_product("z_mid",&create_atmosphere_diagnostic<VerticalLayerDiagnostic>);
-  diag_factory.register_product("geopotential_int",&create_atmosphere_diagnostic<VerticalLayerDiagnostic>);
-  diag_factory.register_product("geopotential_mid",&create_atmosphere_diagnostic<VerticalLayerDiagnostic>);
-  diag_factory.register_product("height_int",&create_atmosphere_diagnostic<VerticalLayerDiagnostic>);
-  diag_factory.register_product("height_mid",&create_atmosphere_diagnostic<VerticalLayerDiagnostic>);
-  diag_factory.register_product("dz",&create_atmosphere_diagnostic<VerticalLayerDiagnostic>);
   diag_factory.register_product("DryStaticEnergy",&create_atmosphere_diagnostic<DryStaticEnergyDiagnostic>);
   diag_factory.register_product("SeaLevelPressure",&create_atmosphere_diagnostic<SeaLevelPressureDiagnostic>);
   diag_factory.register_product("WaterPath",&create_atmosphere_diagnostic<WaterPathDiagnostic>);
   diag_factory.register_product("ShortwaveCloudForcing",&create_atmosphere_diagnostic<ShortwaveCloudForcingDiagnostic>);
   diag_factory.register_product("LongwaveCloudForcing",&create_atmosphere_diagnostic<LongwaveCloudForcingDiagnostic>);
   diag_factory.register_product("RelativeHumidity",&create_atmosphere_diagnostic<RelativeHumidityDiagnostic>);
   diag_factory.register_product("VaporFlux",&create_atmosphere_diagnostic<VaporFluxDiagnostic>);
+  diag_factory.register_product("VerticalLayer",&create_atmosphere_diagnostic<VerticalLayerDiagnostic>);
   diag_factory.register_product("precip_surf_mass_flux",&create_atmosphere_diagnostic<PrecipSurfMassFlux>);
   diag_factory.register_product("surface_upward_latent_heat_flux",&create_atmosphere_diagnostic<SurfaceUpwardLatentHeatFlux>);
   diag_factory.register_product("wind_speed",&create_atmosphere_diagnostic<WindSpeed>);
@@ -60,4 +54,5 @@ inline void register_diagnostics () {
 }
 
 } // namespace scream
+
 #endif // SCREAM_REGISTER_DIAGNOSTICS_HPP

components/eamxx/src/diagnostics/tests/CMakeLists.txt

@@ -1,77 +1,73 @@
-# NOTE: tests inside this if statement won't be built in a baselines-only build
+include(ScreamUtils)
 
 function (createDiagTest test_name test_srcs)
   CreateUnitTest(${test_name} "${test_srcs}"
     LIBS diagnostics physics_share
     LABELS diagnostics)
 endfunction ()
 
-if (NOT SCREAM_ONLY_GENERATE_BASELINES)
-  include(ScreamUtils)
+# Test extracting a single level of a field
+CreateDiagTest(field_at_level "field_at_level_tests.cpp")
 
-  # Test extracting a single level of a field
-  CreateDiagTest(field_at_level "field_at_level_tests.cpp")
+# Test interpolating a field onto a single pressure level
+CreateDiagTest(field_at_pressure_level "field_at_pressure_level_tests.cpp")
 
-  # Test interpolating a field onto a single pressure level
-  CreateDiagTest(field_at_pressure_level "field_at_pressure_level_tests.cpp")
-  # Test interpolating a field at a specific height
-  CreateDiagTest(field_at_height "field_at_height_tests.cpp")
+# Test interpolating a field at a specific height
+CreateDiagTest(field_at_height "field_at_height_tests.cpp")
 
-  # Test potential temperature diagnostic
-  CreateDiagTest(potential_temperature "potential_temperature_test.cpp")
+# Test potential temperature diagnostic
+CreateDiagTest(potential_temperature "potential_temperature_test.cpp")
 
-  # Test exner diagnostic
-  CreateDiagTest(exner_function "exner_test.cpp")
+# Test exner diagnostic
+CreateDiagTest(exner_function "exner_test.cpp")
 
-  # Test virtual temperature
-  CreateDiagTest(virtual_temperature "virtual_temperature_test.cpp")
+# Test virtual temperature
+CreateDiagTest(virtual_temperature "virtual_temperature_test.cpp")
 
-  # Test atmosphere density
-  CreateDiagTest(atmosphere_density "atm_density_test.cpp")
+# Test atmosphere density
+CreateDiagTest(atmosphere_density "atm_density_test.cpp")
 
-  # Test vertical layer (dz, z_int, z_mid)
-  CreateDiagTest(vertical_layer "vertical_layer_tests.cpp")
+# Test vertical layer (dz, z_int, z_mid)
+CreateDiagTest(vertical_layer "vertical_layer_tests.cpp")
 
-  # Test dry static energy
-  CreateDiagTest(dry_static_energy "dry_static_energy_test.cpp")
+# Test dry static energy
+CreateDiagTest(dry_static_energy "dry_static_energy_test.cpp")
 
-  # Test sea level pressure
-  CreateDiagTest(sea_level_pressure "sea_level_pressure_test.cpp")
+# Test sea level pressure
+CreateDiagTest(sea_level_pressure "sea_level_pressure_test.cpp")
 
-  # Test total water path
-  CreateDiagTest(water_path "water_path_tests.cpp")
+# Test total water path
+CreateDiagTest(water_path "water_path_tests.cpp")
 
-  # Test shortwave cloud forcing
-  CreateDiagTest(shortwave_cloud_forcing "shortwave_cloud_forcing_tests.cpp")
+# Test shortwave cloud forcing
+CreateDiagTest(shortwave_cloud_forcing "shortwave_cloud_forcing_tests.cpp")
 
-  # Test longwave cloud forcing
-  CreateDiagTest(longwave_cloud_forcing "longwave_cloud_forcing_tests.cpp")
+# Test longwave cloud forcing
+CreateDiagTest(longwave_cloud_forcing "longwave_cloud_forcing_tests.cpp")
 
-  # Test Relative Humidity
-  CreateDiagTest(relative_humidity "relative_humidity_tests.cpp")
+# Test Relative Humidity
+CreateDiagTest(relative_humidity "relative_humidity_tests.cpp")
 
-  # Test Vapor Flux
-  CreateDiagTest(vapor_flux "vapor_flux_tests.cpp")
+# Test Vapor Flux
+CreateDiagTest(vapor_flux "vapor_flux_tests.cpp")
 
-  # Test precipitation mass surface flux
-  CreateDiagTest(precip_surf_mass_flux "precip_surf_mass_flux_tests.cpp")
+# Test precipitation mass surface flux
+CreateDiagTest(precip_surf_mass_flux "precip_surf_mass_flux_tests.cpp")
 
-  # Test surface latent heat flux
-  CreateDiagTest(surface_upward_latent_heat_flux "surf_upward_latent_heat_flux_tests.cpp")
+# Test surface latent heat flux
+CreateDiagTest(surface_upward_latent_heat_flux "surf_upward_latent_heat_flux_tests.cpp")
 
-  # Test wind speed diagnostic
-  CreateDiagTest(wind_speed "wind_speed_tests.cpp")
+# Test wind speed diagnostic
+CreateDiagTest(wind_speed "wind_speed_tests.cpp")
 
-  # Test AODVIS
-  CreateDiagTest(aodvis "aodvis_test.cpp")
+# Test AODVIS
+CreateDiagTest(aodvis "aodvis_test.cpp")
 
-  # Test "number" paths
-  CreateDiagTest(number_paths "number_paths_tests.cpp")
+# Test "number" paths
+CreateDiagTest(number_paths "number_paths_tests.cpp")
 
-  # Test AEROCOM_CLD
-  CreateDiagTest(aerocom_cld "aerocom_cld_test.cpp")
+# Test AEROCOM_CLD
+CreateDiagTest(aerocom_cld "aerocom_cld_test.cpp")
 
-  # Test atm_tend
-  CreateDiagTest(atm_backtend "atm_backtend_test.cpp")
-
-endif()
+# Test atm_tend
+CreateDiagTest(atm_backtend "atm_backtend_test.cpp")