EAMxx: rely more on Field methods in scorpio output

[bartgol]

The output class is gigantic, but a lot of lines are to deal with update of the views. Instead, we can realy more on the Field class, to perform update, including masking.

[bartgol]

I already started to do some work on this, and one hour already got me quite a lot of work done. I think I'll be able to have something ready for a draft PR early next week. A little sneak-peak: this is the core of the output class update of the tallies, average handling, and call to scorpio. Some methods (like Field::max) will be introduced in the branch.

  for (auto const& name : m_fields_names) {
    // Get all the info for this field.
    const auto& f_in  = m_field_mgrs[AfterHRemap]->get_field(name);
    const auto& f_out = m_field_mgrs[Scorpio]->get_field(name);

    switch (m_avg_type) {
      case OutputAvgType::Instant:
        f_out.deep_copy(f_in);  break;
      case OutputAvgType::Max:
        f_out.max(f_in);        break;
      case OutputAvgType::Min:
        f_out.min(f_in);        break;
      case OutputAvgType::Average:
        f_out.update(f_in,1,1); break;
      default:
        EKAT_ERROR_MSG ("Unexpected/unsupported averaging type.\n");
    }

    if (is_write_step) {
      if (output_step and avg_type==OutputAvgType::Average) {
        // NOTE: we don't divide by the avg cnt for checkpoint output
        if (m_track_avg_cnt) {
          const auto avg_cnt = m_field_to_avg_cnt_map.at(name);

          // We update f_out as "f_out*avg_cnt_inv + avg_cnt_mask" where
          // 
          // avg_cnt_int[i] is
          //   1/avg_cnt[i]    if  avg_cnt[i]>threshold
          //   0               otherwise
          // avg_cnt_mask[i] is
          //   0               if  avg_cnt[i]>threshold
          //   fill_value      otherwise
          // NOTE: the part "+avg_cnt_mask" is only done if the percentage threshold is >0.
          //       If threshold=0, it means we are not worrying about that

          f_out.scale(avg_cnt_inv);
          if (m_avg_coeff_threshold>0) {
            f_out.update(avg_cnt_mask);
          }
        } else {
          // Divide by steps count only when the summation is complete
          f_out.scale(1.0 / nsteps_since_last_output);
        }
      }

      // Bring data to host
      f_out.sync_to_host();

      // Write
      auto func_start = std::chrono::steady_clock::now();
      scorpio::write_var(filename,name,f_out.get_internal_view_data<Real,Host>());
      auto func_finish = std::chrono::steady_clock::now();
      auto duration_loc = std::chrono::duration_cast<std::chrono::milliseconds>(func_finish - func_start);
      duration_write += duration_loc.count();
    }
  }
}