FVCOM使用手册(完整版)

An Unstructured Grid, Finite-Volume Coastal Ocean Model

（无规则网格的有限体积海岸海洋模型）

FVCOM User Manual

（FVCOM用户手册）

FVCOM软件用户许可协议 ........................................................................................................... 3 第一章 序言 ............................................................................................................................... 4 第二章：模型公式 ........................................................................................................................... 6

2.1 直角坐标系下的原始方程 ................................................................................................ 7 2.2 ?-坐标下的控制方程 .................................................................................................... 12 2.3 二维（垂直积分）方程 .................................................................................................. 13 2.4 湍流闭合模型 .................................................................................................................. 15

2.4.1 水平扩散系数 ....................................................................................................... 15 2.4.2 垂直旋转粘性和热扩散系数 ............................................................................... 16 2.5 球面坐标系下的原始方程 .............................................................................................. 24 第三章 有限体积离散法 ............................................................................................................... 27

3.1 不规则三角网格的设计 .................................................................................................. 27 3.2 笛卡尔坐标下的离散方法 .............................................................................................. 29

3.2.1 二维外部模式 ....................................................................................................... 29 3.2.2 三维内模式 ........................................................................................................... 37 3.3 外部与内部模式的输运一致性 ...................................................................................... 44 3.4 干/湿处理方法 ................................................................................................................. 46

3.4.1 标准 ....................................................................................................................... 48 3.4.2 Isplit的上限 .......................................................................................................... 52 3.5 球坐标系下的有限体积离散方法 .................................................................................. 57 3.6 岸边界条件的微元处理 .................................................................................................. 63 第四章：外部强迫 ......................................................................................................................... 66

4.1 风应力、热通量和降水/蒸发 ......................................................................................... 66 4.2 潮汐强迫 .......................................................................................................................... 67 4.3 增加海岸或江河流量的方法 .......................................................................................... 69

4.3.1 TCE方法 ............................................................................................................... 69 4.3.2 MCE方法 .............................................................................................................. 72 4.4 水平分辨率和时间步长的规范 ...................................................................................... 74 4.5 通过底部输入地下水 ...................................................................................................... 77

4.5.1 简单盐平衡地下水通量形式 ............................................................................... 77 4.5.2 地下水输入的完全格式 ....................................................................................... 78

第五章：开边界处理 ..................................................................................................................... 79

5.1 开边界处理的初始设定 .................................................................................................. 79 5.2 普遍辐射开边界条件 ...................................................................................................... 82 5.3 新的有限体积开边界条件模块 ...................................................................................... 87 第六章：数据同化方法 ................................................................................................................. 97

6.1 推导方法 ........................................................................................................................ 100 6.2 OI方法 .......................................................................................................................... 102

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6.3 Kalman筛选 ................................................................................................................... 104

6.3.1减小序列Kalman筛选(RRKF) .......................................................................... 106 6.3.2 集合Kalman筛选(EnKF) .................................................................................. 109 6.3.3 集合平方根Kalman过滤(EnSRF) .................................................................... 111 6.3.4. 集合变换 Kalman筛选 (ETKF) ...................................................................... 113 6.3.5确认实验 .............................................................................................................. 114

第七章：FVCOM沉积模块 ....................................................................................................... 120

7.1 控制方程 ........................................................................................................................ 121 7.2 简单测试情况 ................................................................................................................ 122 第八章：FVCOM生物模块 ....................................................................................................... 123

8.1灵活生物模块（FBM） ................................................................................................ 124

8.1.1 FBM流程图 ........................................................................................................ 124 8.1.2 FBM中的方程和函数 ........................................................................................ 126 8.2 提前选择生物模块 ........................................................................................................ 157

8.2.1 养分-浮游植物-浮游动物（NPZ模型） .......................................................... 158 8.2.2 磷限制低养分层食物网模型 ............................................................................. 160 8.2.3. The Multi-Species NPZD Model ........................................................................ 168 8.2.3 多物种NPZD模型 ............................................................................................ 168 8.2.4 水质量模型 ......................................................................................................... 171

第九章：示踪-追踪模型 ............................................................................................................. 174 第十章：三维拉格朗日粒子追踪 ............................................................................................... 175 第十二章：代码平行 ................................................................................................................... 193

12.1 区域分解 ..................................................................................................................... 194 12.2 区域设置 ..................................................................................................................... 195 12.3 数据交换 ..................................................................................................................... 196 12.4数据收集 ...................................................................................................................... 197 12.5 执行 ............................................................................................................................. 198 第十三章：模型代码描述和总说明 ........................................................................................... 199

13.1 在使用FVCOM前的用户应知 ..................................................................................... 199 13.3 数值稳定的标准 ......................................................................................................... 206 13.4子程序和函数描述 ...................................................................................................... 207 第14章 模式安装，编译和运行 ............................................................................................... 231

14.1 获得FVCOM .................................................................................................................. 232

14.2a 编译METIS库 .................................................................................................. 233 14.2b 编译FVCOM .................................................................................................... 233 14.3a 运行FVCOM（连续） ..................................................................................... 238 14.3b 运行FVCOM（平行） ..................................................................................... 239

第十五章：模型设置 ................................................................................................................... 240

15.1 FVCOM运行时间控制变量文件casename_run.dat .................................................. 240 15.2 FVCOM输入文件 .......................................................................................................... 253 15.3特殊设置的必需输入文件 .......................................................................................... 256 15.4 原始输入文件的输入文件格式 ................................................................................. 257 15.5 建立和使用FVCOM模块 ............................................................................................. 268 第十六章：FVCOM测试例子 ................................................................................................... 292

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第十七章：不规则三角形网格产生 ........................................................................................... 319

17.1数据准备 ...................................................................................................................... 320 17.2 网格产生 ..................................................................................................................... 324 感谢 .............................................................................................................................................. 347 参考文献....................................................................................................................................... 348

FVCOM Software Users’ License Agreement

FVCOM软件用户许可协议

All users should read this agreement carefully. A user, who receives any version of the source code of FVCOM, must accept all the terms and conditions of this

agreement and also agree that this agreement is like any written negotiated agreement signed by you. You may be required to have another written agreement directly with Dr. Changsheng Chen at SMAST/UMASS-D and Dr. Robert C. Beardsley at WHOI

所有用户须仔细阅读此协议。收到FVCOM源代码译本的用户必须接受本协议的所有条款并与陈常胜博士和罗伯特C.比尔兹利博士直接签署书面协议。

The Finite-Volume Coastal Ocean Model (―FVCOM‖) source code has been developed in the Marine Ecosystem Dynamics Modeling Laboratory led by Dr. C. Chen at the University of Massachusetts – Dartmouth (UMASS-D) in collaboration with Dr. R. Beardsley at the Woods Hole Oceanographic Institution. All copyrights to the FVCOM code are reserved. Unauthorized reproduction and redistribution of this code are expressly prohibited except as allowed in this License.

有限体积海岸海洋模型（FVCOM）源代码由陈常胜博士领导的马萨诸塞州达特默斯大学海洋生态动力学模型实验室与伍兹霍尔海洋学协会的罗伯特C.比尔兹利博士合作开发。我们保留FVCOM代码的所有版权，在未经许可的情况下禁止复制和重新分配本代码。

A. Permitted Use and Restrictions on Redistribution

The user agrees that he/she will use the FVCOM source code, and any

modifications to the FVCOM source code that the user may create, solely for internal, non-commercial purposes and shall not distribute or transfer the FVCOM source code or modifications to it to any person or third parties not participating in their primary research project without prior written permission from Dr. Chen. The term

\other scholarly research which (a) is not undertaken for profit, or (b) is not intended to produce work, services, or data for commercial use.

A． 对于重新分配的许可使用和限制

用户须同意使用FVCOM源代码，可以对源代码做出的个人的，非商业性的修改，不得传播或转让FVCOM源代码 ，不得将修改的源代码给没有预先与陈常胜博士签署书面协议任何人或没有参加主要研究工作的第三方。在最终用户许可协议中使用的“非商业性”的意思是（a）不获得利润或（b）不用以商业用途的生产、服务、数据的理论或学术研究。

B. Mandatory Participation in the FVCOM Community

The user agrees to openly participate in the FVCOM community through three primary mechanisms. These are (a) reporting code bugs and problems, (b) sharing

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major modifications made to the code, and (c) contributing to an open and ongoing discussion of model deficiencies, needed improvements and additions, and major

successes. (Contact Drs. C. Chen, G. Cowles, or R. Beardsley). These mechanisms are intended to benefit the entire FVCOM user community through quick notification of code problems, possible solutions, major code improvements, and, in general, the further development of the FVCOM source code and the associated software tools needed to process, visualize and interpret FVCOM model output.

B．参与FVCOM社区

用户可以通过三种主要途径公开参与FVCOM社区（a）报告代码缺陷和问题（b）分享对代码的修正（c）公开讨论模式缺陷、必须的改进和增加以及主要成就（与陈常胜博士或罗伯特C.比尔兹利博士接触）。通过这些途径可以使整个FVCOM社区快速通知用户代码问题、可能的解决方法、主要代码改进、FVCOM源代码和程序所需要的联合软件工具进一步改进、显示和解释FVCOM模式输出。

C. FVCOM Validation

The user agrees to inform Dr. Chen about any FVCOM model validation test case conducted by the user before formal publication of the test case results. This step is intended to minimize potential errors in gridding, model setup, boundary conditions and coding that could contribute to poor FVCOM performance in the validation test case. There is no intent here to exercise any prior restraint on publication.

C． FVCOM确认

用户在测试结果正式出版以前可以通知陈常胜博士任何FVCOM模式确认测试情况。这一步可以减少网格、模式设置、边界条件和译码的潜在错误以改善FVCOM模式确认测试的性能。这些不受出版的限制。

D. Publication of FVCOM Results

The user agrees to acknowledge FVCOM in any publications resulting from the use of the FVCOM source code. The user agrees to use the name ―FVCOM‖ to refer to the model.

D． FVCOM结果的发布

用户发表由FVCOM源程序得到的结果时必须注明并用“FVCOM”来指代模式。

Chapter 1: Introduction

第一章 序言

Throughout much of the world oceans, the inner continental shelves and estuaries are characterized by barrier island complexes, inlets, and extensive intertidal salt marshes. Such an irregularly-shaped ocean-land margin system presents a serious challenge for oceanographers involved in model development even though the governing equations of ocean circulation are well defined and numerically solvable in terms of discrete mathematics. Two numerical methods have been widely used in ocean circulation models: (1) the finite-difference method (Blumberg and Mellor, 1987; Blumberg, 1994; Haidvogel et al., 2000) and (2) the finite-element method (Lynch and Naimie, 1993; Naimie, 1996). The finite-difference method is the most basic discrete scheme

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and has the advantage of computational and coding efficiency. Introducing an

orthogonal or non-orthogonal curvilinear horizontal coordinate transformation into a finite-difference model can provide adequate boundary fitting in relatively simple coastal regions but these transformations are incapable of resolving the highly irregular inner shelf/estuarine geometries found in many coastal areas (Blumberg 1994; Chen et al. 2001; Chen et al. 2004a). The greatest advantage of the

finite-element method is its geometric flexibility. Triangular grid meshes of arbitrary spatially-dependent size are commonly used in this method, and can provide an

accurate fitting of the irregular coastal boundary. The P-type Finite-Element Method (Maday and Patera, 1988) or Discontinuous Galerkin Method (Reed and Hill, 1973; Cockburn et al., 1998) has recently been applied to ocean and have shown promise in improving both computational accuracy and efficiency.

全球海洋内部大陆架和河口有复杂的礁岛、水湾、广阔的高潮线与低潮线之间的盐碱湾等特征。即使定义并可用离散数学解得大洋环流控制方程，这种不规则的海岸边界系统对于研究模型发展的海洋学家是一个严峻的挑战。有两种常用的数学方法解决大洋环流模型：（1）有限差分方法（Blumberg and Mellor, 1987; Blumberg, 1994;Haidvogel et al., 2000）（2）有限元方法(Lynch and Naimie, 1993;Naimie, 1996)。有限差分法基于离散方法并具有计算和编码效率的优点。在有限差分法中引入正交或非正交水平曲线坐标转换可以为简单海岸区域提供适当的边界，但这种转换不能解决许多海岸的高度不规则内部陆架/河口几何学(Blumberg 1994; Chen et al. 2001; Chen et al.2004a)。有限元法最大的优点是几何学的灵活性。任意空间尺寸的三角网格通常用于这种方法，并可精确的适用于不规则海岸边界。P型有限元法(Maday and Patera, 1988)或不连续Galerkin方法(Reed and Hill, 1973; Cockburn et al., 1998)已应用于解决海洋问题并取得了较好的计算精确性和效率。

We have developed a 3-D unstructured-grid, free-surface, primitive equation, Finite-Volume Coastal Ocean circulation Model (called FVCOM) (Chen et al. 2003a; Chen et al.2004b). Unlike the differential form used in finite-difference and finite-element models, FVCOM discretizes the integral form of the governing equations. Since these integral equations can be solved numerically by flux

calculation (like those used in the finite-difference method) over an arbitrarily-sized triangular mesh (like those used in the finite-element method), the finite-volume

approach is better suited to guarantee mass conservation in both the individual control element and the entire computational domain. From a technical point of view,

FVCOM combines the best attributes of finite-difference methods for simple discrete coding and computational efficiency and finite-element methods for geometric flexibility. This model has been successfully applied to study several estuarine and shelf regions that feature complex irregular coastline and topographic geometry, including inter-tidal flooding and drying (see http://codfish.smast.umassd.edu or http://fvcom.smast.umassd.edu for descriptions of these initial applications).

我们开发了三维自由网格、自由表面、原始方程、有限体积海岸大洋环流模型（FVCOM）(Chen et al. 2003a; Chen et al.2004b).与有限差分法和有限元法使用的微分形式不同，FVCOM是对控制方程进行离散。在自由尺度三角网格中（与有限元方法相同）用通量计算（与有限差分法相同）可以从数学上解得这些积分方程，有限体积近似可以保证单独控制要素和整体计算范围的质量守恒。从技术角度来看，FVCOM结合了用于简单离散编码和计算功率的有限差分法以及用于几何灵活性的有限元法的优良特征。这种模型已成功应用于研究几种河口

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