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Fix and standardize parameters.md — notation, tables, units, and row numbering (#203)
* fixes the conflation of soil and microbial maintenance respiration by splitting * formated the file with clang * Fix and standardize parameters.md — notation, tables, units, and row numbering * changes * All missing parameter symbols have been successfully added to parameters.md * Fix clang-format alignment on soilMaintRespiration assignment (lines 1178-1179) * Fix clang-format continuation indentation on soilMaintRespiration assignment Use ContinuationIndentWidth (base + 4 spaces) instead of AlignOperands for multi-line assignment continuation on lines 1178-1179. * Fix clang-format style: operator-first continuation line formatting Move the * operator to the start of the continuation line (lines 1178-1179) to comply with clang-format style guidelines. * fixes * clang-format * updated the parameter.md file * Align parameters docs with issue #81 scope and PR feedback * Remove sipnet.c and state.h changes from PR203 * Align parameters.md with model-structure scope * Mark non-implemented params with fraktur notation * Update docs/parameters.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update docs/parameters.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update docs/parameters.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * capitalize "notes" Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * capitalize "notes" Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update docs/parameters.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * capitalize "notes" Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * replace degree symbol with \circ Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fix eqn refs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * consistent caps for RH RA * Clarify transpiration notation and leaf-water cap docs * Update docs/parameters.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update docs/parameters.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * changes as suggested by maintainer updated parameters.md and model-structure * Apply suggestion from @dlebauer * Apply suggestion from @dlebauer * Address unresolved PR 203 notation and parameter doc comments --------- Co-authored-by: David LeBauer <dlebauer@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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docs/model-structure.md

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@@ -737,10 +737,9 @@ $F^W_{\text{precip,soil}}$ is added to soil water in \eqref{eq:Braswell_A4}.
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ET = E + T
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\end{equation}
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Evapotranspiration ($ET$) is calculated as the sum of evaporation ($E$) and transpiration ($T$), which are defined
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below:
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Evapotranspiration ($ET$) is calculated as the sum of evaporation ($E$) and transpiration ($T=F^W_{\text{trans}}$). These fluxes are defined below:
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### Evaporation
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#### Evaporation
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There are two components of evaporation: (1) immediate evaporation from intercepted precipitation or canopy irrigation
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and (2) soil surface evaporation.
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F^W_{\text{intercept,evap}} = f_{\text{intercept}}\,(F^W_{\text{precip}} + F^W_{\text{irrig,canopy}})
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\end{equation}
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##### Canopy interception evaporation (optional leaf water pool)
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If `LEAF_WATER` is enabled (CLI: `--leaf-water`), SIPNET limits immediate evaporation from canopy interception
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using an LAI-scaled cap on the interception-evaporation flux. In `calcPrecip()`, potential interception evaporation is:
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\begin{equation}
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E_{\text{int,pot}} = f_{\text{intercept}} \cdot F^W_{\text{precip}}
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\end{equation}
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and is capped by an LAI-scaled maximum interception-evaporation flux:
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\begin{equation}
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E_{\text{int,max}} = LAI \cdot WHC_{\text{leaf}}
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\end{equation}
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so that:
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\begin{equation}
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E_{\text{int}} = \min(E_{\text{int,pot}}, E_{\text{int,max}})
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\end{equation}
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Any rainfall not evaporated immediately becomes throughfall to the soil.
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**Soil Evaporation**
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Soil evaporation is computed as:
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Negative (condensation) values are clipped to zero. If snow > 0 then $F^W_{\text{soil,evap}}=0$.
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#### Evaporation
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#### Total Evaporation
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Total evaporation is calculated as the sum of intercepted water, soil evaporation, and sublimation:
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\begin{equation}
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E = F^W_{\text{trans}} + F^W_{\text{intercept,evap}} + F^W_{\text{soil,evap}} + F^W_{\text{sublim}}
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E = F^W_{\text{intercept,evap}} + F^W_{\text{soil,evap}} + F^W_{\text{sublim}}
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\end{equation}
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### Transpiration
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#### Potential Transpiration
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\begin{equation}
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T_{\text{pot}} = \frac{\text{GPP}_{\text{pot}}}{\text{WUE}}
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F^W_{\text{trans,pot}} = \frac{\text{GPP}_{\text{pot}}}{\text{WUE}}
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\label{eq:Braswell_A14}
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\end{equation}
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This is equation (A14) from Braswell, et al. (2005).
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Potential transpiration $(T_{\text{pot}})$ is calculated as the potential gross primary
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Potential transpiration $(F^W_{\text{trans,pot}})$ is calculated as the potential gross primary
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production $(\text{GPP}_{\text{pot}})$ divided by WUE.
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#### Actual Transpiration
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This is equation (A15) from Braswell, et al. (2005).
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Actual transpiration $(F^W_\text{trans})$ is the minimum of potential transpiration $(F^W_{\text{pot}})$ and the
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Actual transpiration $(F^W_\text{trans})$ is the minimum of potential transpiration $(F^W_{\text{trans,pot}})$ and the
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fraction $(f)$ of the total soil water $(W_\text{soil})$ that is removable in one day.
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## Dependence Functions for Temperature and Moisture

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