Abstract
About this manual and MRI.COM
This technical report is a manual of the Meteorological Research Institute Community Ocean Model (MRI.COM).
MRI.COM is an ocean general circulation model developed and maintained at the Meteorological Research Institute(MRI) of the Japan Meteorological Agency (JMA). It has been used for studying large scale oceanic phenomena and as
the oceanic part of the coupled climate models developed at MRI. Recently, it is expanding its coverage to coastal small
scale phenomena.
The current version of MRI.COM is version 4. Version 1 (developed around 2000) was intended to present a prototype.
Eﬀorts were devoted to combining the two ocean models used until then in MRI. For this reason, users at that time tended tobe restricted to MRI research scientists who were committed to the development. Thus, users were deeply knowledgeable
about the model.
Version 2 (early 2000s) was intended for use in the operational forecasting system in JMA. Since the number of users
without direct experience in developing models was expected to increase, the developers decided to write a detailed manualfor that version. The Japanese version was published in 2005 (Ishikawa et al., 2005) and eventually became the prototypeof this manual.
Version 3 was intended for use as an oceanic component of the Earth System Model of MRI (MRI-ESM1; Yukimotoet al., 2011). One of the reasons for creating a new version was that the definition of vertical grid arrangement wasmodified during the development. MRI participated in the Coupled Model Intercomparison Project Phase 5 (CMIP5)
using MRI-ESM1, and its results on the future projection were expected to be used by a wide range of communities, so a
detailed description of its oceanic component was prepared in English (Tsujino et al., 2010).
Version 4 is intended for use as the oceanic part of the next operational forecasting systems of JMA as well as a newEarth System Model of MRI (MRI-ESM2) prepared for the Coupled Model Intercomparison Project Phase 6 (CMIP6).
This version includes the following improvements.
• Tide producing potential and inverse barometer eﬀect of surface atmospheric pressure are introduced into thedepth-integrated (barotropic) equations, considering an application to coastal processes. The linear response of thesystem to the tide producing potential is calculated separately from the other processes, so that self-attraction andloading aﬀect only tidal processes.
• A vertically rescaled height coordinate (z ∗ coordinate; Adcroft and Campin, 2004) has been introduced.
• Nesting function has been expanded. Oﬀ-line (parent and child models are executed serially) one-way, on-line(parent and child models are executed in parallel) one-way and two-way nesting become possible. In on-line
two-way nesting, sea water volume and scalar quantities can be conserved for a system of parent and child models.
• Program files are classified into several packages to ease the maintenance. Each package is made as independent as
possible from other ones and is controlled by a driver program, which is named as package_ctl.F90.
• The user interface is entirely revised. Specifically, monitoring and sampling functions have been expanded, several
input and output files use a format diﬀerent than the previous versions so that their contents can be checkedeasily, and the block names and the contents of namelists are renamed so that they are more self-explanatory. See
READMEs for details.
Note that the purpose of this manual is to present a detailed description of a particular model system. The mathematicalexpressions of processes, the parameterization methods, and the numerical algorithms presented here follow those adopted
in the latest code. They are largely state-of-the-art, but this does not necessarily mean that they are the complete reflectionsof physical, mathematical, and numerical integrity. Every method is subject to possible sophistication. We welcome
critical comments and suggestions from any reader or user, which are necessary for further improvement.
For a more general or detailed description of OGCMs, please refer to textbooks by Griﬃes (2004) and Kantha andClayson (2000). The former thoroughly describes the fundamentals of OGCMs, and the latter concisely summarizes themodeling of various oceanic processes such as tide and sea ice.
–v–Organization
Chapter 1 introduces OGCMs and MRI.COM. It also presents the classification of OGCMs and the status of MRI.COM
with respect to the state-of-the-art OGCMs.
Part I describes the model configuration. Governing equations are derived in Chapter 2, and the spatial grid arrangement
is explained in Chapter 3.
Part II describes the solution procedures of diagnostic equations. Chapter 4 presents definition of the equation of stateof sea water. Chapter 5 presents definition of the continuity equations for unit grid cells.
Part III describes the solution procedures of momentum equation. The method of solving the barotropic and thebaroclinic part of the momentum equation are presented in Chapters 6 and 7, respectively.
Part IV describes the method of solving the advection-diﬀusion equation for tracers. Chapter 8 presents advection
schemes. Subgrid-scale parameterizations for horizontal and vertical mixing are explained in Chapters 9 and 10, respectively. Biogeochemical models are presented in Chapter 11 and inert tracers are explained in Chapter 12. Chapter 13
explains usage of the tracer package.
Part V describes boundary processes. Surface fluxes are presented in Chapter 14. Surface mixed-layer models arepresented in Chapter 15. Bottom boundary layer parameterization is explained in Chapter 16. Sea ice part is explained inChapter 17. How to construct and run a pair of nested-grid models is presented in Chapter 18.
Part VI contains miscellaneous topics. Basics of the finite diﬀerence method are presented in Chapter 19, generalorthogonal curvilinear coordinates and related calculus are introduced in Chapter 20, and finally user’s guide to construct
and run a model is presented in Chapter 21.
Each chapter is almost independent from other chapters. Thus the readers might be able to understand the contents ofeach chapter without referring to other chapters. However, reading Part I will give the readers the background to help
understand the remainder of this manual.
The following are some comments about the notations used throughout this manual. The characters and expressions
in Courier fonts are adopted from program codes. The subscripts and indices used in discrete equations are intended toexpress staggered grid arrangements. They do not necessarily correspond to the array indices in program codes.

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