EAMxx: alias only outputs, fix docs

Author: mahf708

components/eamxx/docs/user/io_aliases.md

@@ -26,11 +26,11 @@ alias_name:=internal_field_name
 ### Basic Usage
 
 ```yaml
-        field_names:
-          - "LWP:=LiqWaterPath"      # Alias LWP for LiqWaterPath
-          - "SWP:=SolidWaterPath"    # Alias SWP for SolidWaterPath  
-          - "T:=T_mid"               # Alias T for T_mid
-          - "qv"                      # Regular field name (no alias)
+field_names:
+  - "LWP:=LiqWaterPath"      # Alias LWP for LiqWaterPath
+  - "SWP:=SolidWaterPath"    # Alias SWP for SolidWaterPath  
+  - "T:=T_mid"               # Alias T for T_mid
+  - "qv"                     # Regular field name (no alias)
 ```
 
 ### Mixed Usage
@@ -39,9 +39,9 @@ You can mix aliased and non-aliased fields in the same configuration:
 
 ```yaml
 field_names:
-  - "T_mid"                          # Regular field name
+  - "T_mid"                        # Regular field name
   - "LWP:=LiqWaterPath"            # Aliased field
-  - "ps"                            # Regular field name  
+  - "p_mid"                        # Regular field name  
   - "RH:=RelativeHumidity"         # Aliased field
 ```
 
@@ -64,30 +64,13 @@ original field names
    - Memory management uses original field structures
 
 3. **Metadata**: Variable attributes (units, long_name, etc.)
-are preserved from the original fields
-
-## Input Reading
-
-The same alias syntax works for reading input files:
-
-```yaml
-input_streams:
-  initial_conditions:
-    filename: ic_file.nc
-    field_names:
-      - "LWP:=LiqWaterPath"    # Read variable LWP from file into field LiqWaterPath
-      - "T:=T_mid"             # Read variable T from file into field T_mid
-```
-
-## Error Handling
-
-The system provides comprehensive error checking:
+are preserved from the original fields, and `eamxx_name`
+is added to the netcdf files to document aliasing
 
-- **Duplicate Aliases**: Each alias must be unique within a field list
-- **Malformed Syntax**: Proper error messages for invalid alias specifications
-- **Empty Names**: Both alias and field names must be non-empty
+## Caveats
 
-Example error cases:
+Currently, a field can be requested only once in a single stream,
+and either the original name or the alias name counts.
 
 ```yaml
 field_names:

components/eamxx/src/share/io/scorpio_input.cpp

@@ -82,20 +82,7 @@ init (const ekat::ParameterList& params,
       "Error! Input class was already inited.\n");
 
   m_params = params;
-  
-  // Get field specifications and process aliases
-  std::vector<std::string> field_specs = m_params.get<decltype(field_specs)>("field_names");
-  auto [alias_to_field_map, alias_names] = process_field_aliases(field_specs);
-  m_alias_to_field_map = alias_to_field_map;
-  m_alias_names = alias_names;
-  
-  // Extract internal field names for field manager operations
-  m_fields_names.clear();
-  for (const auto& spec : field_specs) {
-    auto [alias, field_name] = parse_field_alias(spec);
-    m_fields_names.push_back(field_name);
-  }
-  
+  m_fields_names = m_params.get<decltype(m_fields_names)>("field_names");
   m_filename = m_params.get<std::string>("filename");
 
   // Sets the internal field mgr, and possibly sets up the remapper
@@ -212,38 +199,35 @@ void AtmosphereInput::read_variables (const int time_index)
   if (m_atm_logger) {
     m_atm_logger->info("[EAMxx::scorpio_input] Reading variables from file");
     m_atm_logger->info("  file name: " + m_filename);
-    m_atm_logger->info("  var names: " + ekat::join(m_alias_names,", "));
+    m_atm_logger->info("  var names: " + ekat::join(m_fields_names,", "));
     if (time_index!=-1) {
       m_atm_logger->info("  time idx : " + std::to_string(time_index));
     }
   }
   EKAT_REQUIRE_MSG (m_fields_inited and m_scorpio_inited,
       "Error! Internal structures not fully inited yet. Did you forget to call 'init(..)'?\n");
 
-  for (size_t i = 0; i < m_fields_names.size(); ++i) {
-    const auto& field_name = m_fields_names[i];
-    const auto& alias_name = m_alias_names[i];
+  for (auto const& name : m_fields_names) {
 
-    auto f_scorpio = m_fm_for_scorpio->get_field(field_name);
-    auto f_user    = m_fm_from_user->get_field(field_name);
+    auto f_scorpio = m_fm_for_scorpio->get_field(name);
+    auto f_user    = m_fm_from_user->get_field(name);
 
-    // Read the data using alias name for netcdf variable
+    // Read the data
     switch (f_scorpio.data_type()) {
       case DataType::DoubleType:
-        scorpio::read_var(m_filename,alias_name,f_scorpio.get_internal_view_data<double,Host>(),time_index);
+        scorpio::read_var(m_filename,name,f_scorpio.get_internal_view_data<double,Host>(),time_index);
         break;
       case DataType::FloatType:
-        scorpio::read_var(m_filename,alias_name,f_scorpio.get_internal_view_data<float,Host>(),time_index);
+        scorpio::read_var(m_filename,name,f_scorpio.get_internal_view_data<float,Host>(),time_index);
         break;
       case DataType::IntType:
-        scorpio::read_var(m_filename,alias_name,f_scorpio.get_internal_view_data<int,Host>(),time_index);
+        scorpio::read_var(m_filename,name,f_scorpio.get_internal_view_data<int,Host>(),time_index);
         break;
       default:
         EKAT_ERROR_MSG (
             "Error! Unsupported/unrecognized data type while reading field from file.\n"
             " - file name : " + m_filename + "\n"
-            " - field name: " + field_name + "\n"
-            " - alias name: " + alias_name + "\n");
+            " - field name: " + name + "\n");
     }
 
     f_scorpio.sync_to_dev();

components/eamxx/src/share/io/scorpio_input.hpp

@@ -3,7 +3,6 @@
 
 #include "share/field/field_manager.hpp"
 #include "share/grid/abstract_grid.hpp"
-#include "share/io/eamxx_io_utils.hpp"
 
 #include "ekat/ekat_parameter_list.hpp"
 #include "ekat/logging/ekat_logger.hpp"
@@ -123,10 +122,6 @@ class AtmosphereInput
   std::string               m_filename;
   std::vector<std::string>  m_fields_names;
 
-  // Field aliasing support
-  std::map<std::string, std::string> m_alias_to_field_map;  // Map from alias names to internal field names
-  std::vector<std::string>           m_alias_names;         // List of alias names (for netcdf variables)
-
   bool m_fields_inited  = false;
   bool m_scorpio_inited = false;
 

components/eamxx/src/share/io/scorpio_output.cpp

@@ -753,8 +753,7 @@ register_variables(const std::string& filename,
 
       // Add alias information if variable name differs from field name
       if (alias_name != field_name) {
-        scorpio::set_attribute(filename, alias_name, "eamxx_alias", alias_name);
-        scorpio::set_attribute(filename, alias_name, "eamxx_field_name", field_name);
+        scorpio::set_attribute(filename, alias_name, "eamxx_name", field_name);
       }
     }
   }

components/eamxx/src/share/util/eamxx_data_interpolation.cpp

@@ -33,6 +33,7 @@ DataInterpolation (const std::shared_ptr<const AbstractGrid>& model_grid,
   using namespace ShortFieldTagsNames;
   m_input_files_dimnames[COL] = "ncol";
   m_input_files_dimnames[LEV] = "lev";
+  e2str(LEV);
 }
 
 void DataInterpolation::run (const util::TimeStamp& ts)