SELFE: A semi-implicit Eulerian–Lagrangian finite-element model for cross-scale ocean circulation

Unstructured-grid models grounded on semi-implicit, finite-volume, Eulerian–Lagrangian algorithms, such as UnTRIM and ELCIRC, have enjoyed considerable success recently in simulating 3D estuarine and coastal circulation. However, opportunities for improving the accuracy of this type of models were identified during extensive simulations of a tightly coupled estuary–plume–shelf system in the Columbia River system. Efforts to improve numerical accuracy resulted in SELFE, a new finite-element model for cross-scale ocean modeling. SELFE retains key benefits, including computational efficiency of existing semi-implicit Eulerian–Lagrangian finite-volume models, but relaxes restrictions on grids, uses higher-order shape functions for elevation, and enables superior flexibility in representing the bathymetry. Better representation of the bathymetry is enabled by a novel, “localized” vertical grid that resembles unstructured grids. At a particular horizontal location, SELFE uses either S coordinates or SZ coordinates, but the equations are consistently solved in Z space. SELFE also performs well relative to volume conservation and spurious oscillations, two problems that plague some finite-element models. This paper introduces SELFE as an open-source code available for community use and enhancement. The main focus here is on describing the formulation of the model and on showing results for a range of progressively demanding benchmark tests. While leaving details to separate publications, we also briefly illustrate the superior performance of SELFE over ELCIRC in a field application to the Columbia River estuary and plume.     

一种基于时延的水下声基阵坐标估算方法

阵形估算是水听器阵列应用中的关键问题,基于时延的水下声基阵大地坐标标定方法利用声源发射和声阵接收的CW脉冲之间的时延获得空间中的三个声源发射点到阵元的距离,并以这三个声源发射点为圆心,以声源发射点到阵元的距离为半径做球面,得到的交点即为阵元的大地坐标.通过实验数据分析结果可以得出如下结论:基于时延的球面交汇法得到的阵形标定结果的绝对误差均值为0.13 m,可以把该方法运用于实际的工程测量当中.     

2012年秋季白脊管藤壶在江苏如东互花米草盐沼向附着及分布

互花米草Spartina alterniflora自1979年引入至今,已在我国海岸带大范围扩张并对盐沼湿地生态系统产生了很大影响.本研究以附着生物藤壶为例,研究了互花米草扩张对附着生物的影响.通过对5个断面共28个样方的米草植株、附着藤壶以及藤壶在互花米草上的最大附着高度调查,获得结果如下:藤壶在互花米草滩上的附着范围位于潮沟两侧,且呈宽度约为5 m的带状分布;潮沟规模越大,其向陆方向的延伸范围越宽;每个站位藤壶附着的相对最大高度都位于同一水平.附着藤壶均为白脊管藤壶Fistulobalanus albicostatus,平均干重237±69g·m-2,大部分藤壶直径在2～10mm之间.互花米草的平均干重为981±81g·m-2,潮沟附近互花米草高壮但密度较小,远离潮沟互花米草矮小但密度较大.分析表明,互花米草为藤壶提供了附着基质,并影响藤壶在潮间带的平面分布格局(尽管藤壶的生态位保持不变).影响白脊管藤壶分布特征的原因主要是海水浸没时间的差异;负地形的浸没时间更有利于藤壶的附着和生存;另外潮沟较高的潮水流速除了利于白脊管藤壶幼体的附着外,还可以通过水流的涨、落为其带来充足的食物.     

The tidal flushing of multiple-loop animal burrows

Tidal flushing of animal burrows in mangrove swamps provides an effective and important mechanism for transport of salt and other soluble substances. The burrows have complex morphologies consisting of multiple loops. Using established computational modelling techniques, burrow geometries were simulated from characteristic burrow dimensions and the effect of multiple loops on flushing is studied. The computational models show that flushing is enhanced in multiple-loop burrows as upper loops can be completely evacuated, increasing the volume of burrow water removed. The models indicate that there may be a depth limit to which flushing occurs in complex burrow structures. Periscope loops extend further than one characteristic loop depth and are shown to affect the flushing of burrows if the surface-water plume penetrates to their lower depth. Periscope loops with surface openings on the downstream side of the burrow, relative to the tidal inundation, most frequently experience this condition and thus have a great impact on burrow flushing. Field measurements of salinity agree with the hypothesis that there is a depth limit of flushing for complex burrows that is independent of burrow salinity, and suggest a value of 30–35 cm. The measurements also support the suggestion that significant flushing of burrows occurs within a single tidal event. An experiment considered the movement of animals across the interface created by low-salinity surface water and high-salinity burrow water after a partial flushing event. The motion enhances the effective diffusion coefficient of salt by a factor of at least 10², as compared with free diffusion of salt in water, resulting in a more even distribution of dissolved salt in the burrow water between tidal inundations. This distribution may lead to an increase in the depth to which flushing occurs during subsequent inundations.     

Coupling of life cycles of the copepods Calanus chilensis and Centropages brachiatus to upwelling induced variability in the central-southern region of Chile

A time series of zooplankton sampling carried out at Station 18 off Concepción (36°S, 73°W) from August 2002 to December 2003 allowed the study of annual life cycles of the copepods Calanus chilensis and Centropages brachiatus in association with environmental variability in the coastal upwelling zone. Changes in the abundance of eggs, nauplii, and copepodids were assessed from samples taken at a mean time interval of ca. 20 days. Upwelling variability in near-surface waters was reflected in seasonal changes in salinity, water column stratification, and oxycline depth, as well as a weak seasonal signal in sea surface temperature (1-2 °C). Both copepods exhibited similar life cycles, characterized by continuous reproduction throughout the year. Estimates of generation times, as a function of temperature, were 25-30 days for C. chilensis and 27-35 days for C. brachiatus, predicting about 12 and 10 generations a year, respectively. These estimates were consistent with reproduction pulses observed in the field. It was thus suggested that copepods may grow under non-limiting food conditions in this upwelling area. However, despite continuous reproduction, there were abrupt changes in population sizes along with the disappearance of early naupliar and copepodid stages taking place even during the upwelling season (spring/summer). These changes were attributed to sudden increases in mortality taking place in spring or early summer, after which the populations remained at low levels through the fall and winter. It is thus suggested that, in addition to variability in the physical environment, biological interactions modulating changes in copepod mortality should be considered for understanding copepod life cycles in highly productive upwelling systems.     

Comparisons between the influences of habitat, body size and season on the dietary composition of the sparid Acanthopagrus latus in a large marine embayment

Seasonal samples from Shark Bay on the west coast of Australia were used to determine (1) the habitats occupied by the juveniles and adults of Acanthopagrus latus in this large subtropical marine embayment and (2) the extent to which the dietary composition of this sparid is influenced by habitat type, body length and season. Sampling was undertaken in two habitat types in which A. latus was known to be abundant, namely mangrove (Avicennia marina) creeks and nearby rocky areas, the latter comprising sandstone boulders and/or limestone reefs. The mean total length ±95% CLs of A. latus was far lower in mangrove creeks, 126 ± 6.1 mm, than in rocky areas, 313 ± 4.7 mm. As A. latus attains maturity at ca. 245 mm, the juveniles of this species typically occupy mangrove areas and then, with increasing body size, move to nearshore rocky areas, where they become adults. The species composition of the food ingested by juvenile A. latus in mangrove creeks differed markedly from that of large juveniles and adults in rocky areas. Based on analyses of data for both habitat types combined, this difference was far greater than that between size classes and season, which was negligible. There were indications, however, that, overall within each habitat, the dietary composition did change seasonally, although not with body size. Acanthopagrus latus fed predominantly on mangrove material, sesarmid crabs and small gastropods in mangrove habitats, and mainly on Brachidontes ustulatus in rocky areas, where this mytilid bivalve is very abundant. The mangrove material, which contributed nearly 40% of its overall dietary volume in mangrove creeks, consisted mainly of lateral root primordia. This apparently unique food source for a teleost is presumably ingested through subsurface nipping, which would be facilitated by the mouth and dentitional characteristics of sparids. The almost total lack of correspondence in the dietary compositions of fish in the length class that was well represented in both mangrove and rocky areas illustrates the extent to which this sparid is capable of opportunistic feeding behaviour.     

Geochemical and hydrodynamic constraints on the distribution of trace metal concentrations in the lagoon of Nouméa, New Caledonia

Seawater samples were collected in the lagoon of Nouméa (southwest New Caledonia) along two transects from eutrophic coastal bays to the oligotrophic barrier reef. Land-based emissions to the lagoon were measured with dissolved and particulate concentrations of chromium (Cr) and nickel (Ni), used as tracers of both terrigenous and industrial (Ni ore treatment) activities, as well as dissolved and particulate concentrations of zinc (Zn), used as a tracer of urban effluents. The spatial variability of metal concentrations was related to geochemical and hydrodynamic conditions, i.e., respectively: (1) natural and anthropogenic emission sources, and chemical processes occurring in the water column; and (2) water residence times. The parameter used to describe the residence time of water masses was the local e-flushing time, i.e. the time required for a tracer mass contained within a given station to be reduced by a factor 1/e. High metal concentrations were found in coastal areas (up to 9000 ng dissolved Ni L⁻¹), and steeply decreased with distance from the coast (down to 101 ng dissolved Ni L⁻¹ near the barrier reef) to reach levels similar to those found in remote Pacific waters, suggesting a rapid renewal of waters close to the barrier. Distributions of metals in the lagoon are controlled upstream by land-based emission sources and later chemical processes. Then hydrodynamics constrain metal distributions, as shown by the observed relationship between local e-flushing times and the spatial variability of metal concentrations. In addition, a change in the direction of prevailing winds yielded a decrease of dissolved metal concentrations at the same site by a factor of 2.5 (Cr and Ni) and 2.9 (Zn). It is suggested that the residence time is a key parameter in the control of elemental concentrations in the lagoon waters, as much as land-based emission sources.     

Correspondence between the distribution of hydrodynamic time parameters and the distribution of biological and chemical variables in a semi-enclosed coral reef lagoon

Hydrodynamic modeling can be used to spatially characterize water renewal rates in coastal ecosystems. Using a hydrodynamic model implemented over the semi-enclosed Southwest coral lagoon of New Caledonia, a recent study computed the flushing lag as the minimum time required for a particle coming from outside the lagoon (open ocean) to reach a specific station [Jouon, A., Douillet, P., Ouillon, S., Fraunié, P., 2006. Calculations of hydrodynamic time parameters in a semi-opened coastal zone using a 3D hydrodynamic model. Continental Shelf Research 26, 1395–1415]. Local e-flushing time was calculated as the time requested to reach a local grid mesh concentration of 1/e from the precedent step. Here we present an attempt to connect physical forcing to biogeochemical functioning of this coastal ecosystem. An array of stations, located in the lagoonal channel as well as in several bays under anthropogenic influence, was sampled during three cruises. We then tested the statistical relationships between the distribution of flushing indices and those of biological and chemical variables. Among the variables tested, silicate, chlorophyll a and bacterial biomass production present the highest correlations with flushing indices. Correlations are higher with local e-flushing times than with flushing lags or the sum of these two indices. In the bays, these variables often deviate from the relationships determined in the main lagoon channel. In the three bays receiving significant riverine inputs, silicate is well above the regression line, whereas data from the bay receiving almost insignificant freshwater inputs generally fit the lagoon channel regressions. Moreover, in the three bays receiving important urban and industrial effluents, chlorophyll a and bacterial production of biomass generally display values exceeding the lagoon channel regression trends whereas in the bay under moderate anthropogenic influence values follow the regressions obtained in the lagoon channel. The South West lagoon of New Caledonia can hence be viewed as a coastal mesotrophic ecosystem that is flushed by oligotrophic oceanic waters which subsequently replace the lagoonal waters with water considerably impoverished in resources for microbial growth. This flushing was high enough during the periods of study to influence the distribution of phytoplankton biomass, bacterial production of biomass and silicate concentrations in the lagoon channel as well as in some of the bay areas.     

用单片机实现水声遥控指令的脉冲周期编码（PTC）信号

本文介绍用单片机实现脉冲周期编码（ＰＴＣ）的电路,给出硬件和软件的配置,其特点是灵活、简单、可靠,适合用于水下传输多个声遥控指令     

南海北部表层颗粒有机碳的季节和年际变化遥感分析

海洋颗粒有机碳（POC）是海洋固碳的一个关键参数。为了研究南海北部陆架及海盆表层POC浓度的时空分布特征以及变化趋势,本文利用2009-2011年4个季节的实测数据,对NASA发布的MODIS/AQUA卫星月平均POC遥感产品,进行了验证和校正;并利用校正后的遥感数据分析了2003-2014年POC的时空分布特征和变化趋势。发现POC遥感产品与南海北部实测数据具有较好的线性关系（R2=0.72）,但存在系统性偏高,需利用实测数据对遥感数据进行区域性校正。分析校正后的遥感数据发现,南海北部陆架POC浓度较高,平均为（33.34±8.02）mg/m3;吕宋海峡西南海域浓度较低,平均为（29.25±6.20）mg/m3;中央海盆区浓度最低,平均为（27.02±4.84）mg/m3。春夏季POC浓度较低,最低值一般出现在5月,冬季（12月至翌年1月）POC浓度达到最高。利用2003-2014年的长时间序列遥感叶绿素（Chl a）和海表温度（SST）、混合层深度（MLD）模式数据,以及实测数据对南海北部POC浓度的影响机制进行了分析。发现POC与Chl a在秋冬呈现较好的相关关系（R2=0.51）,但在春夏季较离散,表明秋冬季生物作用对POC影响较大。2003-2014年期间,POC与Chl a、MLD及SST存在明显的年际变化,但并没有显著的上升或下降趋势。