Atlantis User Guide - Part I

• 0. FOREWARD
• 1. INTRODUCTION
• 2. INSTALLATION AND RUNNING
• 3. GEOMETRY OF THE MODEL DOMAIN
• 4. HYDRODYNAMIC, SALINITY AND TEMPERATURE FORCING DATA
• 5. THE PHYSICS SUBMODEL
• 6. DEFINITIONS OF FUNCTIONAL GROUPS
• 7. RUN PARAMETERS
• 8. FORCE PARAMETERS
• 9. PRIMARY PRODUCER PROCESSES
• 10. CONSUMER PROCESSES
• 11. DISTRIBUTION AND MOVEMENT
• 12. PROCESSES IN BACTERIAL AND INANIMATE POOLS
• 13. INFLUENCE OF ENVIRONMENTAL FACTORS ON ECOLOGICAL PROCESSES
• 14. FINAL OVERVIEW OF ECOLOGY ROUTINES
• REFERENCES
• Appendix 1: TIPS FOR CALIBRATING BIOLOGICAL MODEL: NOTES FROM THE 2015 ATLANTIS SUMMIT