Fix #290: Add documentation for SMD method and FcPhoto issues

[sunt05]

Summary

This PR adds comprehensive documentation to help users understand and troubleshoot near-zero FcPhoto (photosynthesis flux) values that can occur in summer when using SMD method 0.

Background

Issue #290 reported that FcPhoto values were unexpectedly close to 0 during summer months (May-September) when they should be at their highest. The user discovered that switching from SMD method 0 to method 1 (with observed soil moisture data) resolved the issue.

Changes Made

1. Enhanced Troubleshooting Guide

Added a new section "FcPhoto (Photosynthesis Flux) Near Zero in Summer" in docs/source/troubleshooting.rst that includes:

• Clear problem description and symptoms
• Root cause explanation (soil moisture stress shutting down photosynthesis)
• Detailed background on how environmental stress factors affect FcPhoto
• Multiple solution approaches for both SMD method 0 and methods 1/2
• Step-by-step diagnostic procedures
• Prevention strategies for new simulations

2. Improved SMD Method Documentation

Updated docs/source/inputs/tables/RunControl/csv-table/SMDMethod.csv to:

• Add warnings about potential FcPhoto issues with method 0
• Emphasise the importance of proper soil moisture initialisation
• Highlight method 1 as a recommended solution for sites with soil moisture observations
• Provide detailed considerations and advantages for each method

Technical Details

The issue occurs because SMD method 0 uses an internal soil water balance model. When soil moisture becomes too low (due to poor initialisation or high evapotranspiration), the soil moisture stress factor (g_smd) approaches 0, which causes FcPhoto to approach 0 through the equation:

FcPhoto = -Fc_Photo * gfunc
where gfunc = g_dq * g_ta * g_smd * g_kdown

Testing

Documentation changes only - no code modifications. The enhanced documentation provides:

• Clear guidance for users experiencing this issue
• Preventive measures for new users setting up simulations
• Better understanding of the relationship between soil moisture and biogenic CO2 fluxes

Checklist

• Documentation follows the project style
• Addresses the specific issue reported in SUEWS FcPhoto output in summer close to 0 #290
• Provides both immediate solutions and long-term prevention strategies
• Cross-references between configuration and troubleshooting sections
• Uses British English as per project guidelines

Fixes #290