PSyclone is a source-to-source Fortran compiler designed to programmatically optimize, parallelize, and instrument HPC applications via user-provided transformation scripts. These scripts allow for a clear separation of concerns between the scientific model, described in Fortran, and the optimization choices. This separation improves the maintainability of complex scientific applications by enabling independent exploration and development of each aspect. In addition, it provides a solution to achieve better performance portability for Fortran applications by encoding the transformations that are beneficial to each platform and compiler in different transformation scripts.</p> <p>PSyclone supports two modes of operation. The first mode optimizes existing source code, including MPI-based applications, by making the necessary code transformations to effectively use the capabilities and programming models supported by each CPU and GPU vendor. This approach is demonstrated using a benchmark extracted from the NEMO ocean model. The second mode defines a kernel-based parallelism model with domain-specific Fortran-embedded metadata. This approach enables a stricter separation of concerns, thereby allowing PSyclone to take full control of the data dependencies and iteration spaces in order to improve its capabilities and generate distributed and shared-memory parallelism. This approach has been co-designed with the Met Office and is used in the Finite-Element based dynamical core of the LFRic atmospheric model.