A system generates a customized application data structure for modeling physical systems. The system includes a processor, an input device, optionally a display device, and a memory device. The processor is adapted to embed a multiphysics model data structure in the application data structure. The multiphysics model data structure comprises a representation of models of physical systems. Geometry data representing geometry subroutines and call data representing geometry subroutine calls are added to the embedded multiphysics model data structure. Data representing application features are added to the application data structure. Each application feature comprises one or more of (i) first data representing a form feature, or (ii) second data representing an action feature. A customized application data structure is generated providing a customized modeling of the physical systems using a modeling operation, a geometry of the one or more models of physical systems, an application feature, and a geometry subroutine. The customized application data structure is configured for distribution to end users as an application executed by an application runtime engine.