AMAPSim is a well-regarded software in this field, and it offers a range of capabilities that might align well with your project's objectives.

Capabilities:
Structural Modeling: AMAPSim excels in simulating the 3D structure of plants, including branches, leaves, and roots.

Light Interception: The software can model how light interacts with the plant, including how much light is absorbed by each leaf, which is crucial for your energy balance considerations.

Botanical Theory: AMAPSim is grounded in botanical theory, which means it aims to be as realistic as possible in terms of plant physiology and morphology.

Parameter Customization: You can customize various parameters to suit the specific species of plant you are studying.

Time-Step Simulation: The software allows you to simulate plant growth over time, which can be useful for long-term studies.

Data Export: AMAPSim allows you to export the data for further analysis, which can be beneficial if you're looking to integrate this model with other systems or studies.

Limitations:
Learning Curve: The software can be complex to learn, especially if you're not familiar with plant modeling or botanical theory.

Computational Resources: Depending on the complexity of your model, AMAPSim can be resource-intensive, requiring a powerful computer for smooth operation.

Cost: Being a specialized software, it might come with a significant price tag, especially for commercial licenses.

Limited to Structural Aspects: While it does a great job with structural modeling and light interactions, it may not include other environmental factors like soil quality, pests, or diseases unless integrated with other software or data sets.

Software Updates: Depending on how actively it's being developed, you might find some features to be outdated or lacking in comparison to newer software.

Given your interest in modeling not just the 3D structure but also the energy balance based on light interception, AMAPSim seems like a strong candidate. However, you may need to supplement it with additional tools or data sets to capture all the environmental variables you're interested in.

Would you like to explore more about how to get started with AMAPSim or perhaps delve into a different software package?
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