EAMxx: some diag fixes and docs

components/eamxx/docs/user/diags/conditional_sampling.md

@@ -1,4 +1,4 @@
-# Conditional sampling
+# Conditional sampling diagnostics
 
 The conditional sampling diagnostic allows you to extract field values
 where a specified condition is met, filling other locations with a
@@ -55,7 +55,7 @@ Use the special condition field name `lev`.
 
 Count the number of grid points where a condition is met.
 Use the special input field name `count`. The output will be `1.0`
-where the condition is satisfied and the fill value elsewhere.
+where the condition is satisfied and `0.0` elsewhere.
 This is particularly useful when combined with horizontal or vertical
 reductions to count occurrences of specific conditions.
 

components/eamxx/docs/user/diags/index.md

@@ -7,6 +7,8 @@ are designed generically and composably, and are requestable by users.
 ## Available diagnostics
 
 - [Field contraction](field_contraction.md)
+- [Conditional sampling](conditional_sampling.md)
 - [Binary arithmetics](binary_ops.md)
+- [Vertical derivative](vertical_derivative.md)
 
 More details to follow.

components/eamxx/docs/user/io_aliases.md

@@ -1,4 +1,4 @@
-# EAMxx Field Aliasing Feature
+# Field Aliasing
 
 This document demonstrates the field aliasing feature for EAMxx I/O operations.
 
@@ -52,16 +52,16 @@ When using aliases:
 1. **NetCDF Variables**: The netcdf file will contain variables
 named according to the aliases
 
-   - `LWP` instead of `LiqWaterPath`
-   - `T` instead of `T_mid`
-   - `RH` instead of `RelativeHumidity`
+    - `LWP` instead of `LiqWaterPath`
+    - `T` instead of `T_mid`
+    - `RH` instead of `RelativeHumidity`
 
 2. **Internal Processing**: All internal model operations use the
 original field names
 
-   - Field validation uses `LiqWaterPath`, `T_mid`, etc.
-   - Diagnostic calculations use original names
-   - Memory management uses original field structures
+    - Field validation uses `LiqWaterPath`, `T_mid`, etc.
+    - Diagnostic calculations use original names
+    - Memory management uses original field structures
 
 3. **Metadata**: Variable attributes (units, long_name, etc.)
 are preserved from the original fields, and `eamxx_name`

components/eamxx/src/diagnostics/conditional_sampling.cpp

@@ -37,8 +37,10 @@ void apply_conditional_sampling_1d(
     const std::string &condition_op, const Real &condition_val,
     const Real &fill_value = constants::fill_value<Real>) {
 
+  // if fill_value is 0, we are counting
+  const auto is_counting = (fill_value == 0);
   const auto output_v    = output_field.get_view<Real *>();
-  const auto mask_v = output_field.get_header().get_extra_data<Field>("mask_data").get_view<Real *>();
+  const auto mask_v = !is_counting ? output_field.get_header().get_extra_data<Field>("mask_data").get_view<Real *>() : output_v;
   const auto input_v     = input_field.get_view<const Real *>();
   const auto condition_v = condition_field.get_view<const Real *>();
 
@@ -59,13 +61,13 @@ void apply_conditional_sampling_1d(
         bool condition_masked = has_condition_mask && (condition_mask_v(idx) == 0);
         if (input_masked || condition_masked) {
           output_v(idx) = fill_value;
-          mask_v(idx) = 0;
+          if (!is_counting) mask_v(idx) = 0;
         } else if (evaluate_condition(condition_v(idx), op_code, condition_val)) {
           output_v(idx) = input_v(idx);
-          mask_v(idx) = 1;
+          if (!is_counting) mask_v(idx) = 1;
         } else {
           output_v(idx) = fill_value;
-          mask_v(idx) = 0;
+          if (!is_counting) mask_v(idx) = 0;
         }
       });
 }
@@ -76,8 +78,11 @@ void apply_conditional_sampling_2d(
     const std::string &condition_op, const Real &condition_val,
     const Real &fill_value = constants::fill_value<Real>) {
 
+  // if fill_value is 0, we are counting
+  const auto is_counting = (fill_value == 0);
+
   const auto output_v    = output_field.get_view<Real **>();
-  const auto mask_v = output_field.get_header().get_extra_data<Field>("mask_data").get_view<Real **>();
+  const auto mask_v = !is_counting ? output_field.get_header().get_extra_data<Field>("mask_data").get_view<Real **>() : output_v;
   const auto input_v     = input_field.get_view<const Real **>();
   const auto condition_v = condition_field.get_view<const Real **>();
 
@@ -102,13 +107,13 @@ void apply_conditional_sampling_2d(
         bool condition_masked = has_condition_mask && (condition_mask_v(icol, ilev) == 0);
         if (input_masked || condition_masked) {
           output_v(icol, ilev) = fill_value;
-          mask_v(icol, ilev) = 0;
+          if (!is_counting) mask_v(icol, ilev) = 0;
         } else if (evaluate_condition(condition_v(icol, ilev), op_code, condition_val)) {
           output_v(icol, ilev) = input_v(icol, ilev);
-          mask_v(icol, ilev) = 1;
+          if (!is_counting) mask_v(icol, ilev) = 1;
         } else {
           output_v(icol, ilev) = fill_value;
-          mask_v(icol, ilev) = 0;
+          if (!is_counting) mask_v(icol, ilev) = 0;
         }
       });
 }
@@ -119,8 +124,11 @@ void apply_conditional_sampling_1d_lev(
     const std::string &condition_op, const Real &condition_val,
     const Real &fill_value = constants::fill_value<Real>) {
 
+  // if fill_value is 0, we are counting
+  const auto is_counting = (fill_value == 0);
+
   const auto output_v = output_field.get_view<Real *>();
-  const auto mask_v = output_field.get_header().get_extra_data<Field>("mask_data").get_view<Real *>();
+  const auto mask_v = !is_counting ? output_field.get_header().get_extra_data<Field>("mask_data").get_view<Real *>() : output_v;
   const auto input_v  = input_field.get_view<const Real *>();
 
   // Try to get input mask, if present
@@ -140,13 +148,13 @@ void apply_conditional_sampling_1d_lev(
         bool input_masked = has_input_mask && (input_mask_v(idx) == 0);
         if (input_masked) {
           output_v(idx) = fill_value;
-          mask_v(idx) = 0;
+          if (!is_counting) mask_v(idx) = 0;
         } else if (evaluate_condition(level_idx, op_code, condition_val)) {
           output_v(idx) = input_v(idx);
-          mask_v(idx) = 1;
+          if (!is_counting) mask_v(idx) = 1;
         } else {
           output_v(idx) = fill_value;
-          mask_v(idx) = 0;
+          if (!is_counting) mask_v(idx) = 0;
         }
       });
 }
@@ -157,8 +165,11 @@ void apply_conditional_sampling_2d_lev(
     const std::string &condition_op, const Real &condition_val,
     const Real &fill_value = constants::fill_value<Real>) {
 
+  // if fill_value is 0, we are counting
+  const auto is_counting = (fill_value == 0);
+
   const auto output_v = output_field.get_view<Real **>();
-  const auto mask_v = output_field.get_header().get_extra_data<Field>("mask_data").get_view<Real **>();
+  const auto mask_v = !is_counting ? output_field.get_header().get_extra_data<Field>("mask_data").get_view<Real **>() : output_v;
   const auto input_v  = input_field.get_view<const Real **>();
 
   // Try to get input mask, if present
@@ -181,13 +192,13 @@ void apply_conditional_sampling_2d_lev(
         bool input_masked = has_input_mask && (input_mask_v(icol, ilev) == 0);
         if (input_masked) {
           output_v(icol, ilev) = fill_value;
-          mask_v(icol, ilev) = 0;
+          if (!is_counting) mask_v(icol, ilev) = 0;
         } else if (evaluate_condition(level_idx, op_code, condition_val)) {
           output_v(icol, ilev) = input_v(icol, ilev);
-          mask_v(icol, ilev) = 1;
+          if (!is_counting) mask_v(icol, ilev) = 1;
         } else {
           output_v(icol, ilev) = fill_value;
-          mask_v(icol, ilev) = 0;
+          if (!is_counting) mask_v(icol, ilev) = 0;
         }
       });
 }
@@ -259,17 +270,14 @@ void ConditionalSampling::initialize_impl(const RunType /*run_type*/) {
 
   const auto var_fill_value = constants::fill_value<Real>;
   m_mask_val = m_params.get<double>("mask_value", var_fill_value);
-
-  m_diagnostic_output.get_header().set_extra_data("mask_data", diag_mask);
-  m_diagnostic_output.get_header().set_extra_data("mask_value", m_mask_val);
-
+  if (m_input_f != "count") {
+    m_diagnostic_output.get_header().set_extra_data("mask_data", diag_mask);
+    m_diagnostic_output.get_header().set_extra_data("mask_value", m_mask_val);
+  }
   // Special case: if the input field is "count", let's create a field of 1s
   if (m_input_f == "count") {
     ones = m_diagnostic_output.clone("count_ones");
     ones.deep_copy(1.0);
-    auto ones_mask = ones.clone("count_ones_mask");
-    ones.get_header().set_extra_data("mask_data", ones_mask);
-    ones.get_header().set_extra_data("mask_value", m_mask_val);
   }
 
   // Special case: if condition field is "lev", we don't need to check layout compatibility
@@ -308,7 +316,7 @@ void ConditionalSampling::compute_diagnostic_impl() {
                    "Valid operators are: eq, ==, ne, !=, gt, >, ge, >=, lt, <, le, <=\n");
 
   // Get the fill value from constants
-  const Real fill_value = m_mask_val;
+  const Real fill_value = (m_input_f == "count") ? 0.0 : m_mask_val;
 
   // Determine field layout and apply appropriate conditional sampling
   const auto &layout = f.get_header().get_identifier().get_layout();

components/eamxx/src/diagnostics/tests/conditional_sampling_test.cpp

@@ -296,13 +296,13 @@ TEST_CASE("conditional_sampling") {
     auto qc12_v = qc12.get_view<const Real *, Host>();
     auto qc21_v = qc21.get_view<const Real **, Host>();
 
-    // Check the results - count should be 1.0 where condition is met, fill_value otherwise
+    // Check the results - count should be 1.0 where condition is met, 0 otherwise
     for (int ilev = 0; ilev < nlevs; ++ilev) {
       // check count for qc12
       if (qc12_v(ilev) > comp_val) {
         REQUIRE(count_diag12_v(ilev) == 1.0);
       } else {
-        REQUIRE(count_diag12_v(ilev) == fill_value);
+        REQUIRE(count_diag12_v(ilev) == 0.0);
       }
     }
 
@@ -311,21 +311,21 @@ TEST_CASE("conditional_sampling") {
       if (qc11_v(icol) > comp_val) {
         REQUIRE(count_diag11_v(icol) == 1.0);
       } else {
-        REQUIRE(count_diag11_v(icol) == fill_value);
+        REQUIRE(count_diag11_v(icol) == 0.0);
       }
 
       for (int ilev = 0; ilev < nlevs; ++ilev) {
         // check count for qc21
         if (qc21_v(icol, ilev) > comp_val) {
           REQUIRE(count_diag21_v(icol, ilev) == 1.0);
         } else {
-          REQUIRE(count_diag21_v(icol, ilev) == fill_value);
+          REQUIRE(count_diag21_v(icol, ilev) == 0.0);
         }
         // check count again, but the negative
         if (qc21_v(icol, ilev) <= comp_val) {
           REQUIRE_FALSE(count_diag21_v(icol, ilev) == 1.0);
         } else {
-          REQUIRE_FALSE(count_diag21_v(icol, ilev) == fill_value);
+          REQUIRE_FALSE(count_diag21_v(icol, ilev) == 0.0);
         }
       }
     }