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Linux beginner on ocean science
hailunhe 2017-9-5 17:25
With the background story that many students majored in mathematics or physics during the undergraduate study, I always feel necessary to write something for the beginners of oceanic sciences, aiming to improve their basic scientific skill on the specific research area. It is not surprising that the atmospheric and oceanic sciences share some common features, for example, they both treat the earth-based four dimensional data-sets. In other word, longitude, latitude, depth, and time are the natural coordinates which we need to project the data into, and also where we extract data from. We can imagine the difficulty during the data delivery without a common data format. As a result, the atmospheric and oceanic communities developed and shared an specified storage method, i.e. netcdf format. I suggest my student abandon their window system, and move forward into the linux system. There are a variety of linux systems, and among them, the opensuse, ubuntu, redhat, fedora are the widely-used linux system among my surrounding colleagues. We can not realize an scientific computing without some compilers of computational language. It is well-known that fortran language prevails in the earth science community. Fortunately, we can easily get the free distributed fortran compilers gfortran, or it is natural born in some linux systems. It is noted that gcc (compiler of C language) and g++ (compiler of C++ language) are the other two components besides gfortran in the GNU compiler sets. Once the GNU compilers were installed in your computer, you can install the netcdf in your system, with the guideline in the websites, as http://www.unidata.ucar.edu/ and there are some examples of fortran/C/C++ scripts for reading or writing netcdf files: http://www.unidata.ucar.edu/software/netcdf/examples/programs/ You also need write a Makefile for a project, which help the computer maintain and link the source files, see website: http://www.chinaunix.net/old_jh/23/408225.html Finally, we need some software help us visualization in the data post-processing, and I recommend the powerful and professional tool, NCL, which stands for the NCAR Command Language . It is not easy to install the software from the source files, and I always download the binary directly, like ncl_ncarg-6.2.0.Linux_RHEL6.2_x86_64_nodap_gcc472.tar.gz For more information, visiting http://www.ncl.ucar.edu/ Happy modelling.
个人分类: earth_science|2235 次阅读|0 个评论
[转载]Preventing climate change by increasing ocean alk...
zuojun 2017-8-12 04:01
https://eos.org/editors-vox/preventing-climate-change-by-increasing-ocean-alkalinity?utm_source=eosutm_medium=emailutm_campaign=EosBuzz081117 By Phil Renforth on 9 August 2017 The oceans contain more carbon than soils, plants, animals and the atmosphere combined. Every cubic meter of seawater contains about 120 grams of negatively charged bicarbonate ions, which are balanced with positive ions such as calcium and magnesium. This carbon pool was created naturally over millions of years by mineral weathering. A recent review article published in Reviews of Geophysics explores the possibility of accelerating weathering processes to increase bicarbonate ions in the ocean, and thus prevent climate change and potentially ameliorate ocean acidification. The editors asked one of the authors some questions about the scientific basis for this idea and how it might work in practice. How can the oceans help prevent climate change? About a quarter of our current carbon dioxide (CO 2 ) emissions in the atmosphere are absorbed by the oceans. This has caused a slight decrease in pH levels, a process known as “ ocean acidification .” If we ceased emissions today, the oceans would eventually absorb most of the emitted CO 2 but the acidification would be neutralized by the dissolution of carbonate sediments. This would take thousands of years. Small perturbations in the chemistry of the global oceans is thought to be responsible for some of the climate variability of the past. That also means that it may be possible for us now to artificially alter ocean chemistry to reduce the impacts of climate change. An increase in ocean alkalinity could be achieved by dissolving rocks and minerals either directly in the open ocean or through engineered systems. This would lead to a build-up of calcium, magnesium, or sodium ions in seawater and thus an uptake of CO 2 to form bicarbonate ions. This long-term storage of carbon in order to mitigate climate change is known as “carbon sequestration.” What is the capacity of the oceans to sequester carbon? We emit approximately 40 billion metric tons of CO 2 every year, and our cumulative emissions over the next 100 years may be in the order of a trillion metric tons. Global carbon cycle modelling suggests that the ocean has the capacity to store carbon on this scale with minimal global environmental impact. This storage capacity is similar to underground injection of CO 2 , a practice which is already taking place in some countries. It may be possible to sequester additional carbon, but the environmental impact may become unacceptable. What are the advantages of carbon sequestration in the ocean? The idea of dissolving minerals to sequester CO 2 has been around since the early 1990s. The initial work focused on dissolving silicate rocks in high temperature/pressure reactors to form mineral carbonates. For every mole of calcium/magnesium that precipitates as a carbonate mineral, one mole of CO 2 is sequestered. By increasing alkalinity, every mole of calcium/magnesium is balanced by nearly 2 moles of bicarbonate ions. This means that the engineering requirements may be substantially less per net ton of CO 2 sequestered. It is also possible to dissolve carbonate minerals to form alkaline, bicarbonate-rich, solutions. The rates of carbonate mineral dissolution are considerably more favorable than other minerals such as silicates, which again has positive implications for the engineering requirements of the technology. How might higher carbon levels in the ocean affect ecosystems and marine life? Globally, the environmental impact of increasing ocean alkalinity depends on what concentration of CO 2 is in the atmosphere. If CO 2 is high, then alkalinity addition may help ameliorate the impacts of ocean acidification. Increasing ocean alkalinity also increases the saturation state of carbonate minerals, which, if too low, will negatively impact carbonate-producing organisms in the ocean such as shellfish and coral. The local and regional impact of increasing ocean alkalinity is potentially more acute, and specific to the technology used. For some, this may impact coastal ecosystems, while others are concerned specifically with the open ocean. What are the techniques for increasing carbon storage in the ocean? There are three techniques that may be used to increase ocean alkalinity, and conclusions from early research suggest the technoeconomic cost is comparable to other methods of climate change prevention.
个人分类: My Research Interests|1362 次阅读|0 个评论
RS: algorithm description for NASA ocean color products
haibaraxx 2016-12-16 18:15
The Ocean Biology Processing Group (OBPG) produces and distributes a standard suite of ocean color products for all compatible sensors at Level-2 and Level-3, plus sea surface temperature (SST) products from MODIS. The OBPG also produces a suite of Level-3 evaluation products. Descriptions and references for these standard and evaluation products are provided on http://oceancolor.gsfc.nasa.gov/cms/atbd .
个人分类: Ocean optics|1789 次阅读|0 个评论
11 main tidal constituents of Ocean Tide Loading (OTL)
zhoufcumt 2013-9-18 08:24
11 main tidal constituents of OTL: the semidiurnal M2, S2, K2, and N2 the diurnal K1, O1, P1, and Q1 the long-period M f , M m , and S sa Lunar-only constituents M2, N2, O1, and Q1 Solar-related constituents S2, K2, K1, and P1
个人分类: Tide Displacement|2691 次阅读|0 个评论
My first (and last) OA paper is finally out
热度 2 zuojun 2013-9-14 19:40
Dynamics of the Indian-Ocean oxygen minimum zones http://www.sciencedirect.com/science/article/pii/S007966111300027X ps. We nicknamed it (Indian Ocean) OMZ Bible. Why? Just take a look at Table 1.
个人分类: My Research Interests|2866 次阅读|5 个评论
[转载] Seminar at 清华大学 地学中心
zuojun 2013-5-13 10:59
Time: 5 月14 日下午 1:30 pm Place: 清华大学 地学中心 610 会议室 Title: Dynamics of Oxygen Minimum Zones in the Northern Indian Ocean Speaker: Dr. Zuojun Yu (University of Hawaii)
个人分类: My Research Interests|2182 次阅读|0 个评论
[转载] Webcast: CESM Ocean Model Working Group Meeting
zuojun 2013-1-23 02:52
CESM Ocean Model Working Group Meeting (was live but is over): http://www.fin.ucar.edu/it/mms/ml-live.htm ps. Here is the program: OMWGagenda13.pdf pps: Some of the ppt files will be available o n th e Web. When I receive the inof, I will add it here .
个人分类: My Research Interests|2132 次阅读|0 个评论
Ecosystem survey in the Arctic Ocean
热度 1 Jimcandy 2012-8-13 07:20
Ecosystem survey in the Arctic Ocean
I'm conducting the ecosystem survey in the Arctic Oceanonboard the USicebreaker "Healy" during 5 to 25 August. Hopefully the survey will going well. I will update the process, if possilbe.
个人分类: 我的科研|3893 次阅读|1 个评论
Decadal variability or 50-year trend?
热度 1 zuojun 2012-6-25 11:38
That is the question I need an answer for. A few days ago, I was convinced by a Nature paper that the tropical Indian Ocean has undergone changes that are consistent with what scientists expected from a warming climate. Today, I found two papers that emphasize decadal variability, at least at 32S. (Why 30S? That's a survey line that we have some data to work on.) I need to know the answer quickly, because I have a proposal deadline. So, I emailed the first author in UK. Hope she will answer me soon...
个人分类: My Research Interests|2875 次阅读|3 个评论
If you are interested in ecosystem modeling (revised)...
zuojun 2012-4-9 15:04
I will be giving a seminar at Xia Da, and Bei Da. I will share my experience in the past four year, from a new comer (ecosystem modeling) to an expert (sort of). Oxygen Minimum Zones in the Northern Indian Ocean Time: 10:00 am on April 25th Place: Room B206 State Key Laboratory of Marine Environmental Science (MEL), Xiamen University Time: 10:00 am on May 3rd Place: Room 576 Department of Atmospheric and Oceanic Sciences Peking University
个人分类: My Research Interests|2594 次阅读|0 个评论
Global cooling...
zuojun 2012-2-10 01:27
It's only 73F in my living room at 7:23 am. I have to put socks on. So, I would say it's a cold winter day in Hawaii. However, I will never agree with those people who think burning oil, gas, and coal is ok. It is NOT ok. One third of the CO2 we release into the atmosphere is absorbed by the world ocean. So, the ocean is becoming more acid. Read about ocean acidification, and you will be as worried as most oceanographers about the future of the Earth.
个人分类: Education|2428 次阅读|0 个评论
[转载]CEO Eric Schmidt's LIFE AFTER GOOGLE
热度 1 zuojun 2011-12-29 10:14
http://www.businessinsider.com/life-after-google-eric-schmidts-60-million-ocean-adventure-2011-2 http://www.schmidtocean.org/
个人分类: From the U.S.|1665 次阅读|2 个评论
[转载]ZHEJIANG OCEAN UNIVERSITY & BLUE REVOLUTION HAWAII ...
zuojun 2011-6-11 13:31
ZHEJIANG OCEAN UNIVERSITY AND BLUE REVOLUTION HAWAII SIGN MOU http://bluerevolutionhawaii.blogspot.com/2011/06/zhejiang-ocean-university-and-blue.html 4. Zhejiang Ocean University was formed in 1988, but already has 15,000 students. A new campus at the coastline is being constructed. I would not be surprised if this someday becomes the pre-eminent ocean institution for the country. A sister city relationship is being discussed between Zhoushan and Honolulu. Hawaii's primary link to China could well in time become these islands, located across the bay and south of Shanghai, for we have very similar interests and are the only island states of our respective countries. ps. I think there are some inaccurate predictions and mistakes in this Blog.
个人分类: Uniquely Hawaii|1816 次阅读|0 个评论
[转载]Oxygen Minimum Zones in the Northern Indian Ocean
zuojun 2011-1-21 03:27
Joint Oceanography-IPRC Seminar Zuojun Yu Associate Researcher International Pacific Research Center University of Hawaii "Oxygen Minimum Zones in the Northern Indian Ocean" Abstract: In the tropics, mid-depth oxygen minimum zones (OMZs) are located in poorly ventilated regions below the thermocline. As a result, surface production can contribute to the strength of OMZs remotely as well as locally. In the northern Indian Ocean, OMZs can be found in the Arabian Sea (ASOMZ) and the Bay of Bengal (BBOMZ), consistent with the distribution pattern of ventilation ages. The intensity of the BBOMZ is moderate, while permanent suboxic condition (O2 ~5 μM) is reached in the Arabian Sea, clearly due in part to local production. The ASOMZ is the second most intense OMZ in the tropical ocean, with near-total depletion of oxygen at depths from 200-1000 m. The lower part of the ASOMZ (below 400 m) indicates a northward intensification, in agreement with the ventilation age revealed by CFC ratio. The upper part of the ASOMZ (above 400 m), however, appears east of the most productive regions along the western boundary, and there is no consensus about what causes this “eastward shift.” In contrast, much less is known about the distribution of BBOMZ. In both sub-basins, the relative roles of physical versus biological processes in generating OMZs have not been fully determined, in part because ocean models often fail to reproduce these OMZs. In this seminar, the speaker will present the latest results of their findings. Thursday January 20, 2011 3:00 p.m. MSB 100 http://www.soest.hawaii.edu/oceanography/seminar.html
个人分类: My Research Interests|1687 次阅读|0 个评论
Introducing TEOS-10 (Absolute Salinity for oceanographers)
zuojun 2010-11-4 05:44
According to TEOS-10 , the official source of information about the Thermodynamic Equation Of Seawater - 2010 (TEOS-10). A significant change compared with past practice is that TEOS-10 uses Absolute Salinity SA (mass fraction of salt in seawater) as opposed to Practical Salinity SP (which is essentially a measure of the conductivity of seawater) to describe the salt content of seawater. Ocean salinities now have units of g/kg. ... Importantly, while Absolute Salinity (g/kg) is the salinity variable that is needed in order to calculate density and other seawater properties, the salinity which should be archived in national data bases continues to be the measured salinity variable, Practical Salinity (PSS-78). To avoid confusion while the use of Practical Salinity in scientific publications is phased out, published values of salinity should be specifically identified as being either Practical Salinity with the symbol SP or Absolute Salinity with the symbol SA. The following news came via US CLIVAR office: Replacement of the EOS-80 definition of Seawater properties with TEOS-10 SCOR/IAPSO Working Group 127 on the Thermodynamics and Equation of State of Seawater has recommended the adoption of a new thermodynamic description of the properties of seawater, called the International Thermodynamic Equation Of Seawater 2010 (TEOS-10 for short). This thermodynamic description of seawater properties, together with the Gibbs function of ice, has been endorsed by SCOR and IAPSO and has been adopted by the Intergovernmental Oceanographic Commission (IOC) at its 25th Assembly in June 2009 to replace EOS-80 as the official description of seawater and ice properties in marine science. The TEOS-10 computer software, the TEOS-10 Manual and many other documents may now be obtained from www.TEOS-10.org A notable difference of TEOS-10 compared with EOS-80 is the adoption of Absolute Salinity to be used in scientific journals to describe the salinity of seawater and to be used as the salinity argument in the TEOS-10 algorithms that give the various thermodynamic properties of seawater. Note, however, that we strongly recommend that the salinity that is reported to national databases remain Practical Salinity as determined on the Practical Salinity Scale of 1978 (suitably updated to ITS-90 temperatures as described in the TEOS-10 Manual). The practice of storing one type of salinity in national databases (Practical Salinity), but using a different type of salinity in publications (Absolute Salinity), is exactly analogous to our present practice with temperature; in situ temperature is stored in databases (since it is the measured quantity), but the temperature variable that is used in publications is a calculated quantity, being either potential temperature or Conservative Temperature.
个人分类: My Research Interests|5633 次阅读|0 个评论
[转载]Ocean Tomo 300?专利指数
yngcan 2010-7-9 17:15
Ocean Tomo 300专利指数 Ocean Tomo 300专利指数 Ocean Tomo 300专利指数(OT300)是首个基于知识产权价值的工业指数,该项指数主要对300家拥有优质专利的公司进行评估,并在纽约-泛欧证券交易所(NYSE Euronext)上发布(纽约-泛欧证券交易所代码:OTPAT)。 历史市场指数虽然与现在市场指数有一定的相似性,但是它不能代表现在市场的实际情况。在过去三十多年的时间里,宏观经济价值已发生了天翻地覆的变化。如下图所示,1975年,在SP500公司价值构成中,超过80%是有形资产,无形资产不到20%。现如今,有形资产和无形资产的比例反过来了,将近80%的公司价值体现在无形资产上。OT300指数目前已成为美国一个主要的经济指标。 业绩 从2006年11月1日到2008年12月30日,OT300指数超过SP500指数460个基本点。OT300指数的出色表现,不仅表明OT300指数已成为衡量美国经济的一个重要基准,同时也向人们证明了客观评估专利价值的重要性,为上市公司提供了更全面、更准确的公司情况。通过10年的回顾比较,发现OT300指数每年会超过SP500指数430个基本点。在被无形资产拉动的全球经济中,可以直觉的得出结论,有了强大专利资本的公司在股票市场会表现更好。 指数结构 OT300指数的构成成分主要从美国股票市场上流动性最强的1000只股票中选取,然后再将范围缩小到拥有专利的公司。这些拥有专利的公司按照风格和规模的不同被分成50个小组,然后通过Ocean Tomo专利评级(PatentRating)系统计算出每个公司的专利价值占公司财务价值的比例,并根据计算出的比例进行排序,每个小组中排在前六位的股票成为指标股,50个小组一共300只股票。 可投资产品 以Ocean Tomo 300专利指数和Ocean Tomo 300专利成长指数为基准形成了两个交易型开放式指数基金(ETF),分别是:Claymore/Ocean Tomo 专利ETF(NYSE Euronext:OTP)和Claymore/Ocean Tomo 成长指数ETF(NYSE Euronext:OTR)。Claymore 顾问有限责任公司作为这两个基金的投资顾问。 在过去的30年里,工业经济直接被认为是知识经济,而知识资本已经逐渐成为资产评级的主导。1975年,固定资产,包括工厂、机器和设备,占市场价值超过了80%。而现在,2007年,固定资产的位置被无形资产代替了,只占到了不到20%,市场价值被知识产权所主导。 http://www.oceantomo.com/index_ot300.html
个人分类: 专利|5008 次阅读|0 个评论
Ocean Park 之精灵水母
papaya313575 2010-2-6 23:29
香港出差二十余日,今天终于有时间去转转Ocean Park 了。 缆车刚到山顶,远远就看见了水母万花筒。脑海中立即呈现《阿凡达》中那生活在潘多拉星球上梦幻精灵美杜莎(Medusa),于是,迫不及待的想进去瞧瞧。 进去后,才发现:原来这也是一个精灵世界! 图1 优雅的水母,名未知 图2 啡海刺水母 图3 太平洋海刺水母 以上都是在各种颜色荧光下的月水母
个人分类: 热带雨林|5437 次阅读|2 个评论

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