MohidWiki - User contributions [en]

Ruby

2008-11-19T11:46:25Z

192.168.20.177: /* Irb */

Ruby is (said to be) a great language. People say that programming is fun again. Everything in Ruby is an object. Strings, floats, integers, regexps, arrays are all objects, and all have their methods and fields.

==Starters==
# [http://www.ruby-lang.org/en/documentation/quickstart/ Ruby in 20 minute]

Install ruby
> sudo apt-get install ruby irb rdoc

==Features==
Here we list the interesting features that make ruby so interesting, besides its interesting programming features. These are the extra tools that make working with [[ruby]] appealing and easy.
# interactive shell (irb),
# extension packages manager (gems),
# documentation generator from in-line comments (rdoc),
# unit-testing framework (utest),
# web-apps development framework (rails),

[[Python]] also possesses all of these features built-in (ipython, install, pydoc, unit-tests and django).

===Irb===
The most interesting thing in shell scripting ([[bash]], [[batch|dos]]) is that you can play right from the shell command line. This is what makes interpreted languages so interesting in the first place. Thus, like [[matlab]] or [[python]] (however, I'm not aware of one for [[perl]]), ruby has an interactive shell called [[#irb|irb]].
Interactive ruby allows to experiment and debug interactively in ruby. Similar (but not so powerful) to [[python|ipython]].
> irb
irb(main):001:0> puts "Hello world!"
Hello world!
=> nil
The most interesting method to call in irb is ''public_methods'' which lists all the object's available methods:
irb(main):001:0> puts 11.public_methods.sort.join(" | ")
% | & | * | ** | + | +@ | - | -@ | / | < | << | <= | <=>
| == | === | =~ | > | >= | >> | [] | ^ | __id__ | __send__
| abs | between? | ceil | chr | class | clone | coerce
| denominator | display | div | divmod | downto | dup | eql?
| equal? | extend | floor | freeze | frozen? | gcd | gcdlcm
| gem | hash | id | id2name | inspect | instance_eval | instance_of?
| instance_variable_defined? | instance_variable_get | instance_variable_set
| instance_variables | integer? | is_a? | kind_of? | lcm | method | methods
| modulo | next | nil? | nonzero? | numerator | object_id | power! | prec
| prec_f | prec_i | pretty_inspect | pretty_print | pretty_print_cycle
| pretty_print_inspect | pretty_print_instance_variables | private_methods
| protected_methods | public_methods | quo | rdiv | remainder | require
| require_gem | respond_to? | round | rpower | send | singleton_method_added
| singleton_methods | size | step | succ | taguri | taguri= | taint | tainted?
| times | to_a | to_bn | to_f | to_i | to_int | to_r | to_s | to_sym | to_yaml
| to_yaml_properties | to_yaml_style | truncate | type | untaint | upto | zero? | | | ~
=> nil

===[[Gems]]===
Requires [http://rubygems.org/ rubygems] to be installed. [[gems|Rubygems]] is the extension manager for ruby. Much like cpan is the extension manager for [[Perl]]. [[Gems]] is more than a packaging manager: it's a library versioning manager too!
[http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-talk/132899 That is also it's achille's heel].

===Rdoc===
Rdoc is the automatic html documentation generator for ruby scripts. Much like javadoc is for java. It requires [[#Starters|rdoc]] to be installed.
> rdoc --main mywork/mywork.rb

===Unit testing===
Unit tests are XP's method of choice to build safe long-lasting software. Still looking to see how these work...

===Rails===
Hopefully we'll get there soon enough...

===Ruby2exe===
[http://www.erikveen.dds.nl/rubyscript2exe/index.html#6.0.0 rubyscript2exe] allows to transform ruby scripts into full-bloated executable programs.

> gem install rubyscript2exe

==Sample code==

===loop===
<code lang=ruby >
object = Array.new(["one", "two", "three", "four"])
object.each do |a|
puts a + "\n"
end
</code>

===array===
<code lang=ruby >
object = ["one", "two", "three", "four"]
target = []
object.each { |a|
target.push(a)
}
puts target
</code>

===i/o===
<code lang=ruby >
if File.exist? "sample.txt"
File.open("sample.txt", "r") { |fs|
while line = fs.gets
puts "Line read was '#{line.chomp}'.\n"
end
fs.close
}
end
</code>
<code lang=ruby >
File.open("sample.txt", "w") { |fw|
fw.puts "Hi, this a new line.\n"
fw.close
}
</code>

===regexp===
<code lang=ruby >
pattern = Regexp.new("[a-z]+", "i")
#or
pattern = /[a-z]+/i
if File.exist? "sample.txt"
File.open("sample.txt", "r") { |fs|
while line = fs.gets
if line.match(pattern)
puts "Line read was '#{line.chomp}'.\n"
end
end
fs.close
}
end
</code>

===method===
<code lang=ruby >
def whatisit?(arg1, arg2="optional")
#Ducktyping: Does it walk like a duck? Does quacks like a duck?
if arg1.responds_to? :capitalize
puts "Then '#{arg1.capitalize}' must be a string.\n"
else
if arg1.responds_to? :modulo && arg1.responds_to? :numerator
puts "Then '#{arg1.to_s}' must be an integer.\n"
else
if arg1.responds_to? :modulo && arg1.responds_to? :truncate
puts "Then '#{arg1.to_s}' must be a float.\n"
end
end
end
puts "Input '#{arg2}' was completely optional.\n"
end
</code>

===class===
<code lang=ruby >
#File checktype.rb
class Checktype

#Constructor
def initialize(arg)
#class Checktype field
@variable = arg
end

#class Checktype method
def isWhat?(arg=@variable)
#Ducktyping: Does it walk like a duck? Does it quack like a duck?
if arg.responds_to? :capitalize
puts "Then '#{arg.capitalize}' must be a string.\n"
else
if arg.responds_to? :modulo && arg.responds_to? :numerator
puts "Then '#{arg.to_s}' must be an integer.\n"
else
if arg.responds_to? :modulo && arg.responds_to? :truncate
puts "Then '#{arg.to_s}' must be a float.\n"
end
end
end
end

end
</code>

<code lang=ruby >
require 'checktype'
somevar = Checktype(23)
somevar.isWhat?
#=> '23' must be an integer
Checktype.isWhat? "Hi"
#=> 'Hi' must be a string
</code>

===Complex examples===
*[[Ruby examples|RootTransform classes]]

==External References==
*[http://www.ruby-lang.org/en/ ruby-lang],
*[http://www.ruby-doc.org/docs/ProgrammingRuby/ Programming Ruby]

[[Category:programming]]
[[Category:linux]]
[[Category:ruby]]

Hydrolight

2008-11-19T10:43:32Z

192.168.20.177: /* ABACBB */

== Introduction ==

Hydrolight is a radiative transfer numerical model that solves the time - independent radiative transfer equation. In order to compute the radiance, Hydrolight requires the inherent optical properties of the water body (IOP's), a chlorophyll profile and the water depth. Hydrolight can be applied in different cases:

* It can be run with modeled input values to generate in – water light fields, which are then used as input in primary productivity models or mixed – layer dynamics.

* It can be run with the IOP’s of different water types to simulate in – water light fields for the purpose of selecting and designing instruments for use in various water types.

* It can be run with assumed IOP’s as input in order to obtain estimates of the signals that would be received by various types or configurations of remote sensors, when flown over different water bodies and under different environmental conditions.

* It can also be used to isolate and remove unwanted contributions to remotely sensed signatures. As spectrometers detect not only the water leaving radiance in which we are interested, but also the sky radiance reflected upward by the sea surface. As Hydrolight separately computes all of these components, it can be used to correct the detected signature for surface reflection effects.

* It can be used in different configurations (IOP’s and boundary conditions) when analyzing experimental data in order to tighten up an existing parameterization.

* It can be used to simulate optical signatures for the purpose of evaluating proposed remote – sensing algorithms for their ability to simulate different environments or for examining the sensitivity of algorithms to simulated noise in the signature.

* It can be used to characterize the background environment in an image. When attempting to extract information about an object in the scene, all of the radiance of the natural environment may be considered noise, with the radiance from the object being the signal. The model can then be used to compute and remove the environmental contribution to the image.

* Hydrolight can be run with historical (climatological) or modeled input data to provide estimates about the marine optical environment during times when remotely sensed or in situ data are not available.

Due to the difference in scales in the ocean ( Lh >>> Lv ), we can consider the ocean as consisting of optically independent patches of waters. We thus obtain patches of homogeneous water body whose optical properties vary only with depth. We can then independently apply a one dimensional radiative transfer model at the center of each patch in order to simulate the entire, horizontally inhomogeneous water body. In the analysis of imaging spectrometer data, one might even apply such a model to the water patch associated with the pixel in the image.

== Main characteristics of Hydrolight ==

Hydrolight is/has

* Time – independent

* Horizontally homogeneous IOP’s and boundary conditions

* Arbitrary depth dependence of IOP’s

* Wavelengths between 350 & 800nm

* Capillary – wave – air – water surface

* Finite or infinitely deep (non – Lambertian) bottom

* Includes all orders of multiple scattering

* Includes Raman scatter by water

* Includes fluorescence by chlorophyll and CDOM

* Includes internal sources such as bioluminescence

* Does not include polarization

* Does not include gravity waves or white caps

The fundamental quality that describes the time - independent, 1D light field in the ocean is the spectral radiance L(z,θ,Φ,λ)in (W/m2.sr.nm), with z the depth, θ the zenithal, polar angle of the sun, Φ the azimuthal angle of the sun and λ the wavelength. An overview of the most important optic properties & their relationship to other variables is given by the figure below.
This figure also learns us we will have to provide Hydrolight with incident radiance, sea state, bottom condition, absorption coefficient a, scattering coefficient b and phase function.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/6fe8430e-de53-4173-966a-510d61df5a0e/2008-11-11_1753.png">
<img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/6fe8430e-de53-4173-966a-510d61df5a0e/2008-11-11_1753.png" width="502" height="520" border="0" />
</a>
</div>
</htm>

The Hydrolight standard quad layout has a nominal angular resolution of Δθ = 10º and ΔΦ = 15º. For mathematical reasons, there is no quad centered on the equator.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/e5d89ca9-e4ae-46d7-8db4-50d30e5c44bc/2008-11-11_1805.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/e5d89ca9-e4ae-46d7-8db4-50d30e5c44bc/2008-11-11_1805.png" width="358" height="353" border="0" /></a>
</div>
</htm>

== How to install Hydrolight ==

# The Lahey Fortran 95 express compiler is a pre - requisite to Hydrolight. It has to be installed and registred before installing Hydrolight.
# Install Hydrolight.
# Paste the "novoteste.for" - file and the "teste.for" - file in the batch - map of the maincode directory.
# Paste the "runlist" - file into the run directory
# Paste the "Inovoteste" and the "Iteste" - files into the batch - map of the run - directory

Done!

== How to use Hydrolight ==

When first using Hydrolight you will need to read the disclaimer and accept the license agreement.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/78e68b34-98e3-45dd-9024-a080689bd3f6/2008-11-12_1535.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/78e68b34-98e3-45dd-9024-a080689bd3f6/2008-11-12_1535.png" width="353" height="394" border="10" /></a>
</div>
</htm>

Then you will have to define a root name in the run identification form. It will be used for all files generated by Hydrolight in this run. You can also enter a descriptive title in this form.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/80ec0140-88c1-49ab-b1c3-bada57eb5b0d/2008-11-12_1543.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/80ec0140-88c1-49ab-b1c3-bada57eb5b0d/2008-11-12_1543.png" width="444" height="412" border="10" /></a>
</div>
</htm>

The parametrization of Hydrolight can be changed by selecting "Change limits"

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/0037db04-75ff-4ea5-9f9f-b4fce826c1ef/2008-11-12_1623.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/0037db04-75ff-4ea5-9f9f-b4fce826c1ef/2008-11-12_1623.png" width="498" height="561" border="0" /></a>
</div>
</htm>

Then we have to select the most accurate calculation method for calculationg IOP's. The total IOP's of a water body are built up as a sum of IOP's attributable to the various components of a water nody. Thus the total absorption coefficient is given by:

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/98a1179c-af12-48e9-87a8-8f98473408b4/2008-11-17_1015.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/98a1179c-af12-48e9-87a8-8f98473408b4/2008-11-17_1015.png" width="201" height="56" border="0" /></a>
</div>
</htm>

Although recent papers have proven that this assumption is no longer essential, Hydrolight distinguishes case 1. waters in with a high concentration of chlorophylle (in comparison to other particles) and case 2. waters in which in organic substances are dominant. The models proposed here will use different calculation methods to calculate the absorption a and the light scattering b. Absorption can be defined as the process in which radient (light) energy is converted into chemical (e.g. photosynthesis) or thermal energy. Lights scattering is the proces wherein the light changes direction (elastic scattering ) and / or wavelength. In case only the wavelength is modified we speak of inelastic scattering (e.g. Raman - scattering , chlorophylle fluorescence). It is thus paramount to understand the behaviour of light in the studied water column before selecting a calculation method and a phase function.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/54469163-63eb-4ffa-92fb-68e8d28f1127/2008-11-17_1017.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/54469163-63eb-4ffa-92fb-68e8d28f1127/2008-11-17_1017.png" width="453" height="550" border="0" /></a>
</div>
</htm>

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/215fe1ae-d1ae-4a8f-9b61-84a3a69c574e/2008-11-12_1542.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/215fe1ae-d1ae-4a8f-9b61-84a3a69c574e/2008-11-12_1542.png" width="516" height="514" border="0" /></a>
</div>
</htm>

=== ABCONST ===

The ABCONST - option will consider a fixed total light absorption coefficient a and a fixed light - scattering coefficient b at a single wavelength for a homogeneous water body. This option should only be used in very shallow, homogeneous waters, where we can consider absorption and diffusion as constants (swimming pool case). It is particularly useful for studies in which the depth is measured as non - dimensional optical depth ζ rather than as geometric depth z in meters. When selecting this option we will also have to define a total light - scattering phase function (see also the figure below). Scattering is often modeled by a power law dependence on wavelength:

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/1c6eebc2-8d50-4e6c-adad-810fd4503776/2008-11-17_1658.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/1c6eebc2-8d50-4e6c-adad-810fd4503776/2008-11-17_1658.png" width="236" height="80" border="0" /></a>
</div>
</html>

With X the concentration, b,λ, m & n the model parameters.
We can choose between:

* Isotropic diffusion phase function(equal in all directions)

* Pure Water, Raleigh diffusion phase function (elastic scattering of light,diam << λ)

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/3ebf7587-35fb-4fee-8a00-ef84a3a7b3b8/2008-11-14_1651.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/3ebf7587-35fb-4fee-8a00-ef84a3a7b3b8/2008-11-14_1651.png" width="242" height="116" border="0" /></a>
</div>
</htm>

* Average particle, [[Petzold phase - function]]

* USER - SUPPLIED file containing the discretised phase function

* Have Hydrolight select a phase function with a bb/b value of ...(backscattering/ scattering relationship that indicates us the probability scattering will occur, When selecting this option. Hydrolight will use the backscatter fraction bb(z,λ)/b(z,λ) to generate a phase function having this backscatter fraction at each depth.)

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/2ca149a5-2a7b-41f1-bed8-a2c1f6fda8d9/2008-11-14_1653.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/2ca149a5-2a7b-41f1-bed8-a2c1f6fda8d9/2008-11-14_1653.png" width="362" height="61" border="0" /></a>
</div>
</htm>

Furthermore, we will also have to specify a wavelength which will be used by bottom and sky models later on.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/78e85747-d2fa-4beb-8617-7faae226a5ea/2008-11-13_1428.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/78e85747-d2fa-4beb-8617-7faae226a5ea/2008-11-13_1428.png" width="527" height="577" border="0" /></a>
</div>
</htm>

Then we have to select whether the model has to apply bioluminescence.
In the ABCONST we can not chose to apply inelastic scattering in stead of bioluminescence. The equation for the elastic scattering is given by;

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/6ab6c0a7-280b-40b4-a58c-dc1cf2a970a0/2008-11-14_1712.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/6ab6c0a7-280b-40b4-a58c-dc1cf2a970a0/2008-11-14_1712.png" width="270" height="98" border="0" /></a>
</div>
</htm>

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/9f839fd1-fd67-40dc-b66c-84087ed9b18d/2008-11-14_1458.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/9f839fd1-fd67-40dc-b66c-84087ed9b18d/2008-11-14_1458.png" width="461" height="464" border="0" /></a>
</div>
</htm>

In the next window we will have to define the Air - Water Surface Boundary Conditions. Whenever entering a new speed, we should press "update values" in order to confirm the newly entered value.
The sky - model part will enable us to parametrize the atmospheric effects on solar radiation.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/83271ba3-0f4c-4fcb-a87c-fb114961a51b/2008-11-14_1500.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/83271ba3-0f4c-4fcb-a87c-fb114961a51b/2008-11-14_1500.png" width="434" height="437" border="0" /></a>
</div>
</htm>

=== ABCASE 1 ===

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/62a2acb8-bc8a-4c36-ad80-e29f80e10a2b/2008-11-17_1702.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/62a2acb8-bc8a-4c36-ad80-e29f80e10a2b/2008-11-17_1702.png" width="497" height="324" border="0" /></a>
</div>
</htm>

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/387e9f18-0701-4d22-a8fe-77c6914ab170/2008-11-17_1703.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/387e9f18-0701-4d22-a8fe-77c6914ab170/2008-11-17_1703.png" width="524" height="361" border="0" /></a>
</div>
</htm>

This model is based on a reformulation (Morel and Maritorena, 2000) of the historical Gordon - Morel Case 1 water model. The absorption coefficient is modeled as the sum of three components:

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/882bdbf4-5c8d-44d3-8e69-021c7f12f472/2008-11-17_1039.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/882bdbf4-5c8d-44d3-8e69-021c7f12f472/2008-11-17_1039.png" width="315" height="48" border="0" /></a>
</div>
</htm>

With aw the absorption by pure water and ap the absorption by chlorophyll - bearing particles and ay the absorption by covarying yellow matter (CDOM). The particle absorption is given by:

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/54cfa4aa-4010-4d72-9387-f50bcaa408a0/2008-11-17_1045.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/54cfa4aa-4010-4d72-9387-f50bcaa408a0/2008-11-17_1045.png" width="264" height="49" border="0" /></a>
</div>
</htm>

where Chl(z) is the user - specified chlorophyll profile in mg Chl /m3
and Achl(λ) is the non - dimensional chlorophyll - specific absorption coefficient given in Prieur and Sathyentranath (1981). Absorption by yellow matter covaries with particle absorption according to

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/335bca47-1487-4dbf-8c75-b50b7e2a3e5a/2008-11-17_1059.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/335bca47-1487-4dbf-8c75-b50b7e2a3e5a/2008-11-17_1059.png" width="388" height="44" border="0" /></a>
</div>
</htm>

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/0309a950-a75b-4894-a39d-66b29c6acb2a/2008-11-17_1704.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/0309a950-a75b-4894-a39d-66b29c6acb2a/2008-11-17_1704.png" width="565" height="432" border="0" /></a>
</div>
</htm>

Absorption by chlorophylle is determined by:

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/c0bb4a08-74ca-45b0-b092-a34054c68d40/2008-11-17_1705.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/c0bb4a08-74ca-45b0-b092-a34054c68d40/2008-11-17_1705.png" width="538" height="565" border="0" /></a>
</div>
</htm>

The phase function consists either of a USER - SUPPLIED routine or is determined by Hydrolight by means of the bb/b - relationship.

The scattering coefficient b for the particles is given by:

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/335bca47-1487-4dbf-8c75-b50b7e2a3e5a/2008-11-17_1059.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/335bca47-1487-4dbf-8c75-b50b7e2a3e5a/2008-11-17_1059.png" width="388" height="44" border="0" /></a>
</div>
</htm>

and the yellow matter is assumed to be non - scattering. In this model, the pure water absorption is taken from Pope and Fry (1997), and the pure water scattering is from Smith and Baker (1981). The user must specify the chlorophyll concentration profile Chl(z) and the scattering phase function for the particles. Note that this model reduces to the pure water case if Chl = 0, which is slightly different than the formulation of Morel and Maritorena (2000), which includes a small amount of yellow matter even in the absence of phytoplankton.

When selecting this option we will also have to define a total light -scattering phase function (see also the figure below). Scattering is often modeled by a power law dependence on wavelength:

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/1c6eebc2-8d50-4e6c-adad-810fd4503776/2008-11-17_1658.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/1c6eebc2-8d50-4e6c-adad-810fd4503776/2008-11-17_1658.png" width="236" height="80" border="0" /></a>
</div>
</html>

With X the concentration, b, λ, m & n the model parameters. The Gordon - Morel (1993)for chlorophyll bearing particles is a special case of the power law model with X = Chl, b0 = 0.3, λ0 = 550nm, m = 1 & n = 0.62.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/aa7005a5-6d07-4046-aba1-ddf579a58c13/2008-11-17_1700.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/aa7005a5-6d07-4046-aba1-ddf579a58c13/2008-11-17_1700.png" width="292" height="59" border="0" /></a>
</div>
</html>

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/d88cc60e-6ec4-4ea1-998b-ede9d0a9f701/2008-11-17_1714.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/d88cc60e-6ec4-4ea1-998b-ede9d0a9f701/2008-11-17_1714.png" width="462" height="461" border="0" /></a>
</div>
</htm>

Bioluminescence is included via a USER - SUPPLIED routine and inelastic scattering should be defined in function of the water type;
chlorophylle fluorescence for CASE 1 waters, CDOM fluorescence for CASE 2 waters and RAMAN - scattering for very clear water. Raman - scattering is the inelastic scattering of light between 550 & 650 nm by water molecules. It is described by :

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/e914ff82-fb72-4337-bfa5-771cf3cb3fdf/2008-11-18_1046.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/e914ff82-fb72-4337-bfa5-771cf3cb3fdf/2008-11-18_1046.png" width="477" height="39" border="0" /></a>
</div>
</htm>

Raman absorption coefficient and Raman scattering coefficient are given by:

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/f0355b51-718d-49d9-99fe-47377293a97d/2008-11-18_1047.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/f0355b51-718d-49d9-99fe-47377293a97d/2008-11-18_1047.png" width="386" height="134" border="0" /></a>
</div>
</htm>

Next we will have to define the band of wavelengths. This can be done by either determining the minimum and the maximum wavelength and the wavelength band interval, by manually introducing wavelength band boundaries or by selecting wavelength bands to a particular ocean color sensor. If you want to validate Hydrolight data with satellite data the last option is recommendable.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/d2f279fb-9082-4294-af56-fbb9d29143ab/2008-11-18_1053.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/d2f279fb-9082-4294-af56-fbb9d29143ab/2008-11-18_1053.png" width="540" height="574" border="0" /></a>
</div>
</htm>

In order to execute a succesful run, Hydrolight must know the incident sky radiance on the sea surface. As this also depends on the state of the sea surface, we will have to provide Hydrolight with the wind speed. In order to calculate the surface radiation , we will have to define the sky model to be used. This can either be a semi - empirical sky model or an idealized sky model. The use of the idealized sky model is advisable in the case of homogeneous or heavily overcasted skies while the semi - empirical model allows for more variation. In the ABCASE 1 - routine we will only be allowed to use the semi - empirical sky model.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/13b0a3fb-d574-484b-90ff-6fd0976e2b63/2008-11-18_1112.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/13b0a3fb-d574-484b-90ff-6fd0976e2b63/2008-11-18_1112.png" width="709" height="446" border="0" /></a>
</div>
</htm>

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/c969c83c-02ed-4984-bd16-57208fdd96ca/2008-11-18_1058.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/c969c83c-02ed-4984-bd16-57208fdd96ca/2008-11-18_1058.png" width="434" height="439" border="0" /></a>
</div>
</htm>

Then we will have to specify the sky conditions to be used with the semi - empirical sky model. The position of the sun is either given by the zenith angle or by specifying our time and location on earth.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/59d953af-02f0-4047-8c50-ae41a4e8571e/2008-11-18_1127.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/59d953af-02f0-4047-8c50-ae41a4e8571e/2008-11-18_1127.png" width="567" height="561" border="0" /></a>
</div>
</htm>

If we choose to do so, we can also modify the atmospheric parameters used by the model by selecting the button "view atmospheric parameters".

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/93cd5d17-10f4-40b5-b43d-7d0fd957b418/2008-11-18_1130.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/93cd5d17-10f4-40b5-b43d-7d0fd957b418/2008-11-18_1130.png" width="461" height="488" border="0" /></a>
</div>
</htm>

Then, in order to calculate the semi - empirical sky radiance, the model will require the sky irradiance which is either directly calculated by RADTRAN - model or read fron a USER SUPPLIED DATA FILE.
The angular pattern of the sky radiance will be acquired from a standard routine in the maincode directory

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/2771ad37-3a2f-4802-b1a4-ebf082ecf917/2008-11-18_1132.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/2771ad37-3a2f-4802-b1a4-ebf082ecf917/2008-11-18_1132.png" width="565" height="465" border="0" /></a>
</div>
</htm>

The path of light through the water will also be influenced by its depth and bottom type. If the bottom is indfinitely deep, we won't have to define a bottom reflectance, as all the light will be absorbed by the water column. In case of a finitely deep water column,we can define a percentage of the incident radiation that will always be reflected (reflection is thus independent of wavelength) or a reflectance dependent on the wavelengt supplied by a USER SUPPLIED FILE which is more realistic. This USER SUPPLIED FILE is mostly supplied bu the Hydrolight library which has a variety of files to describe different bottom types (corals, algae, seagrass).

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/f81886cf-f1df-4a12-b4f3-757885200f58/2008-11-18_1214.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/f81886cf-f1df-4a12-b4f3-757885200f58/2008-11-18_1214.png" width="449" height="359" border="0" /></a>
</div>
</htm>

Finally, Hydrolight will also aks us to provide output depths. We can define up to 50 different output depths. These output depths can either be geometric or optical (though for comparison of data, geometric depths are the most advisable) and are defined by entering a maximum depth and a depth interval or they are manually defined.

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/c2afac10-0274-4f6c-b8f8-0c75fe54d005/2008-11-18_1213.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/c2afac10-0274-4f6c-b8f8-0c75fe54d005/2008-11-18_1213.png" width="446" height="562" border="0" /></a>
</div>
</htm>

=== ABCASE 1H ===

Tha ABCASE 1H - model is an IOP - model based on Haltrin. It is written for Case 1 - waters and includes four components; pure water, large microbial particles, CDOM (colored dissolved organic matter with seperate contributions by fulvic and humic acids) and small mineral particles. The humic and fulvic acids are assumed to be non - scattering and the mineral particles are assumed to be non - absorbing. Each of these components (other than pure water) is parametrized by the chlorophyll concentration. The scattering phase functions for the large microbial (large.dpf) and small mineral (small.dpf) particles are based on Kopelevich:

<htm>
<div style="text-align:center;width:100%">
<a href="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/fc5036d8-d770-467e-8d25-8f3e23f7b350/2008-11-17_1122.png"><img src="http://content.screencast.com/users/Nathalie_Verelst/folders/Jing/media/fc5036d8-d770-467e-8d25-8f3e23f7b350/2008-11-17_1122.png" width="471" height="338" border="0" /></a>
</div>
</htm>

The user will thus only need to supply Hydrolight with the chlorophylle profile in this configuration. The Haltrin ABCASE 1H - model is quite new to the scientific society, as a consequence experience is little and it is important to note that its' calculated IOP's can be considerably different from the calculated IOP's of the ABCASE 1 model.

=== ABCASE 2 model ===

The ABCASE 2 model is a generic four component model that includes pure water, Chlorophylle - bearing particles, CDOM and mineral particles. The routine is designed to allow for a great user customization of the input. This flexibility rendering it suitable for many case 2 - waters. The routine also provides us with an alternative for modeling case 1 waters (e.g. by specifying the microbial and CDOM components as desired and setting the mineral conditions to zero).

=== ABACBB ===

We can also compute light fields using absorption and scattering coefficients as measured by the WETLabs ac - 9 or HiStar instrument. In this case we will have to use the ABACBB model. This IOP - model comprises two components; pure water and everything else (particles and dissolved substances detected by ac - 9). Hydrolight can read borth unfiltered and filtered ac - 9 files. The unfiltered ac - 9 file gives us the total absorption (particles + CDOM) whereas the filtered file only possesses the CDOM - absorption. Providing both files , thus allows us to seperate absorption into particulate and dissolved fractions, which gives important information about the ecosystem. Nonetheless, we should realize that light is only influenced by total absorption coefficient, total scattering coefficient and total phase function. If CDOM is assumed to be non - scattering, partioning the absorption into particulate and dissolved fractions does not change the total a, total b or phase function. Therefore it does not change the elastic scattering solution of radiative transfer equation. In abscence of fluorescence, the light field will thus be exactly the same. To quantify CDOM - fluorescence, we first need to know how the light was absorbed by the CDOM. This can be obtained by selecting the option of including CDOM - fluorescence in the Hydrolight - run. If this is the case, the user can optionally define a data file which will come to contain a and c values from a filtered ac - 9. In most cases, CDOM - fluorescence is merely a small contribution to the total light field.
Another important feature is the option of reading a file that contains backscatter coefficients bb(z,λ)as measured by instruments. If available, Hydrolight can use the backscatter fraction bb(z,λ)/b(z,λ) to generate a phase function having this backscatter fraction at each depth and wavelength.
When ac - 9 and instrument data are used to dynamically determine the phase function according to backscatter fraction, a Fournier - Forand phase function is used. This closed - form, analytical phase function is based on Mie - theory and is parametrized by the real index of refraction of the particles and the slope of the Junge size distribution. By varying the particle index of refraction and size distribution, phase functions can be generated with very small (0.0001)to very large backscatter (0.4) fractions. When dynamically determining the phase function, Hydrolight automatically interpolates within its phase function collection ti generate a phase function at each depth with the needed amount of backscatter.
The only problem with this option is that when solving the radiative transfer equation, Hydrolight considers extremely small steps through the water column. In general, the backscatter fraction will change with every depth step, so that a new phase function should be generated for each depth step. As this would greatly add to runtime, the user interface will require the user to secify a backscatter - change parameter.This is the amount by which the backscatter fraction must change before a new phase function is generated, the default is 0.005 (5%).
The Fournier - Forand phase functions are named by their backscatter fraction. For example the phase function on FFbb0001.dpf has a bb/b of 0.0001, whereas FFbb018.dpf has a bb/b of 0.018.

Important remarks about this option:

* Hydrolight always assumes your instrument data are flawless.

* Even while measuring the IOP's directly, we will still need to provide Hydrolight with a chlorophylle - profile.

[[Category:MOHID Water]]
[[Category:Biogeochemistry]]

Batch

2008-11-11T17:51:15Z

192.168.20.177:

[[Batch]] files are the original ms-dos scripting language. A [[batch file]] is a script that contains a list of ms-dos commands, with one command per line. When you try to execute the batch file, it will execute the ms-dos commands, one after another, waiting for each command to finish before starting the next one.
==Examples==
===For===
The following example will output each line of the text file to the stdout:
> FOR /F %i in (list.txt) DO @echo %~ni

The following example will allow to parse and edit the environment variables:
> for /F %i in ('dir /B /S *_1.dat') do @set fil=%i & copy /Y !fil! !fil:1=2!
'''If you want to write '''FOR''' loops in a batch file instead of the command line, then use '''%%i''' instead of '''%i'''.'''

To place the first line of a file into a variable:
> SET /P _MyVar=<MyFilename.txt

To place the ''last'' line of a file into a variable:
> FOR /F "tokens=*" %A IN (C:\boot.ini) DO SET TestVar=%A

Nested FOR Loops
> FOR /F %a IN (filelist.txt) DO (FOR /F %b IN (salinitytemperature.txt) DO echo %a %b)

Nested FOR loops encapsulated in a batch file
for /F %%a in (%1) do (
for /R %%b in (../*) do (
echo %%a
echo %%b
)
)

==Misc==
===Escaping characters===
<,|,> and % characters are special characters in dos. To escape them use the ^ character or a double %
> echo ^<example^>
<example>
===Displaying blank lines===
Use command echo to display a blank line instead of its default status result
>echo.

==Sample applications==
Here's a combination with a batch file, that creates a clean copy of a MOHID simulation:

> copysimulation MySimulation

#'''copysimulation.bat content'''
#Input argument %1 stands for simulation name
@echo off
set COPYHOME=C:\Program Files\2gif
xcopy %1\*.* %1_copy /E /EXCLUDE:%COPYHOME%\exclui.txt
perl %COPYHOME%/replace.pl 's/%2/\.\.\/\.\./g' *
perl %COPYHOME%/replace.pl 's/\\/\//g' *
@echo on

==External References==
*[http://www.robvanderwoude.com/ntfor.html Batch files tutorial];
*[http://www.ss64.com/nt/for.html for command reference];
*[http://www.ss64.com/nt/ windows nt command-line reference].

[[Category:Windows]]
[[Category:Script]]

Batch file

2008-11-11T17:50:57Z

192.168.20.177:

#REDIRECT[[Batch]]

How to create MOHID timeseries outputs

2008-11-11T17:46:28Z

192.168.20.177: /* Run Kml2Mohid */

In this tutorial we will continue to develop the [[How_to_configure_a_2D_model_forced_with_tide_with_MOHID|previously used]] test-case and we will configure the model so it returns a time serie with the water level at the coordinates of our choice on the domain. These time series can then be compared against tidal stations experimental measurements.

==Step 1 - Define the data-acquisition stations==

===Run Google Earth===
[[Google_Earth#Configure_Google_Earth|Make sure you have Google Earth correctly configured!!]]

*With Google earth, choose the locations where there are tidal stations
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cfbc9e9d-0b21-491a-a718-db046096bb10/2008-10-06_1608.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cfbc9e9d-0b21-491a-a718-db046096bb10/2008-10-06_1608.png" width="597" height="443" border="0" /></a></htm>
Repeat the process for every tidal station.

*Save the google earth placemarks as a kml file
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/2b66937c-6c87-46c4-a3af-08eb92dc3f13/2008-10-06_1612.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/2b66937c-6c87-46c4-a3af-08eb92dc3f13/2008-10-06_1612.png" width="320" height="252" border="0" /></a></htm>

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/8e8fa35f-bc08-4b1a-84ef-f72d7c559345/2008-10-06_1613.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/8e8fa35f-bc08-4b1a-84ef-f72d7c559345/2008-10-06_1613.png" width="563" height="412" border="0" /></a></htm>

===Run Kml2Mohid===

*Get the [[Kml2Mohid]] program, edit a [[batch file]], and run the program
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/4ed24f90-dd2b-49bb-8a12-4c94c4212ab4/2008-09-25_1847.png"></div></htm>

*Successfully run [[Kml2Mohid]] program to convert the google earth placemarks into a points file.
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/629db22c-73c4-4ef8-81b4-b73f94f0216a/2008-09-25_1852.png"></div></htm>

*Sample points (.xyz) file. This what the resulting file should look like:
<begin_xyz>
-9.317324064466845 38.67641458263528 0
<end_xyz>

==Step 2 - Create time serie stations with Mohid GIS==

===Import the xyz file containing the tidal stations===

*In [[Mohid GIS]], from the ''Project'' menu, select ''open''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a576e3b7-c9a2-48d4-a8c8-0a622a905f40/2008-10-06_1550.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a576e3b7-c9a2-48d4-a8c8-0a622a905f40/2008-10-06_1550.png" width="320" height="238" border="0" /></a></htm>

*Select the folder, select the saved GIS project, then click on ''Open'':
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/7deb018a-59f8-4c3d-aba0-85a35a8f270e/2008-10-06_1553.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/7deb018a-59f8-4c3d-aba0-85a35a8f270e/2008-10-06_1553.png" width="563" height="412" border="0" /></a></htm>

*Here's what the opened GIS project should look like
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/c407235c-d1da-4f72-8bbb-9f5966d0197e/2008-10-06_1621.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/c407235c-d1da-4f72-8bbb-9f5966d0197e/2008-10-06_1621.png" width="736" height="337" border="0" /></a></htm>

*From the ''Data Items'' menu select ''Add Data Item''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/f42a1aed-5f6d-4544-a48f-e800db151f07/2008-10-06_1605.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/f42a1aed-5f6d-4544-a48f-e800db151f07/2008-10-06_1605.png" width="351" height="221" border="0" /></a></htm>

*????
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/fb9e5ca5-1216-4c46-bb6d-03d1af06070d/2008-10-06_1624.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/fb9e5ca5-1216-4c46-bb6d-03d1af06070d/2008-10-06_1624.png" width="563" height="412" border="0" /></a></htm>

*Drag'n drop the points layer to the top, then right-click on it, then select ''Properties''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/bc03ca36-48e9-4906-8dd6-72eeb3636b74/2008-10-06_1627.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/bc03ca36-48e9-4906-8dd6-72eeb3636b74/2008-10-06_1627.png" width="361" height="197" border="0" /></a></htm>

*Set the pixel size to 5, then select ''Settings''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/f44682b2-211f-4ce3-aae1-e9b72dd144ff/2008-10-06_1630.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/f44682b2-211f-4ce3-aae1-e9b72dd144ff/2008-10-06_1630.png" width="430" height="351" border="0" /></a></htm>

*Select a color and a pixel size for the points.
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a313a211-46c1-44b5-bad3-8eafda3f322d/2008-10-06_1632.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a313a211-46c1-44b5-bad3-8eafda3f322d/2008-10-06_1632.png" width="496" height="361" border="0" /></a></htm>

*Check that the point is well where it should be on the grid
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/49ac2701-6a2b-4a78-9165-9838ff9b3af5/2008-10-06_1635.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/49ac2701-6a2b-4a78-9165-9838ff9b3af5/2008-10-06_1635.png" width="610" height="292" border="0" /></a></htm>

===Create the MOHID time series===

*From the ''Tools'' menu, select ''Create Grid Time Series''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/2c13bdbb-9642-4f55-bdec-6ff36984de31/2008-10-06_1637.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/2c13bdbb-9642-4f55-bdec-6ff36984de31/2008-10-06_1637.png" width="230" height="355" border="0" /></a></htm>

*Select the grid data layer, select the correct xyz layer, define the folder and a new filename for the time series configuration file, define a 10 minute period outputs interval, then click on ''Ok''.
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/43c60c63-9cca-4b91-9c93-8d9358d4d408/2008-10-06_1640.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/43c60c63-9cca-4b91-9c93-8d9358d4d408/2008-10-06_1640.png" width="368" height="481" border="0" /></a></htm>

*Click ''Ok'' upon success!
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/b9814d5c-5f9b-4d2d-9083-0781cdc10710/2008-10-06_1645.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/b9814d5c-5f9b-4d2d-9083-0781cdc10710/2008-10-06_1645.png" width="291" height="119" border="0" /></a></htm>

*Here's a typical time series configuration file
File generated by Mohid GIS

DT_OUTPUT_TIME : 600
MAX_BUFFER_SIZE : 10000

Based on GridData file : D:\Users\Soussou\GeneralData\kml2gis\cascais.dat

Based on XYZ file : D:\Users\Soussou\GeneralData\kml2gis\cascais.xyz

<BeginTimeSerie>
NAME : Station_ 0
LOCALIZATION_I : 65
LOCALIZATION_J : 127
LOCALIZATION_K : 1
CENTER_CELL_X : -9.31735
CENTER_CELL_Y : 38.67645
ORIGINAL_X : -9.317324
ORIGINAL_Y : 38.67641
<EndTimeSerie>

==Step 3 - Configure the model so as to output time series results==

*Open the GUI project
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cb12f137-4c9c-475d-a89d-ce75713122b0/2008-10-06_1700.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cb12f137-4c9c-475d-a89d-ce75713122b0/2008-10-06_1700.png" width="220" height="175" border="0" /></a></htm>

*Select the MOHID project
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/9d400510-2d0f-49c6-aef0-530157e0aaf0/2008-10-06_1702.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/9d400510-2d0f-49c6-aef0-530157e0aaf0/2008-10-06_1702.png" width="563" height="412" border="0" /></a></htm>

*Open the Hydrodynamic module
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/97d24a5c-f192-449f-ba97-2b4406f2a27b/2008-10-06_1658.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/97d24a5c-f192-449f-ba97-2b4406f2a27b/2008-10-06_1658.png" width="360" height="214" border="0" /></a></htm>

*Add the following lines to the hydrodynamic configuration file, then save and close
TIME_SERIE : 1
TIME_SERIE_LOCATION : D:\Users\Soussou\GeneralData\TimeSeries\StLouisTimeSeries.dat

==Step 4 - Run the model again and inspect the time-serie results==

===Run the model===
If all is correctly configured, and all the input files are double-checked, we can hopefully start running our model!

*Select ''Tools'' from menu, then ''Launch Mohid...''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/6e5c5742-0f44-4538-8d57-9b25886c2acd/2008-10-06_1228.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/6e5c5742-0f44-4538-8d57-9b25886c2acd/2008-10-06_1228.png" width="785" height="231" border="0" /></a></htm>

*Select the ''Run_1'', then select ''Run Mohid'', then select ''Launch after Ok'', then click on ''Ok''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a4180c38-199d-48e8-8e40-e5d0684c0785/2008-10-06_1230.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a4180c38-199d-48e8-8e40-e5d0684c0785/2008-10-06_1230.png" width="616" height="617" border="0" /></a></htm>

*Supervise the screen-outputs to check for any error, or to simply read the estimated end time of simulation
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/f536ea29-1ca2-4929-8dd4-3660f5a5bdb8/2008-10-06_1235.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/f536ea29-1ca2-4929-8dd4-3660f5a5bdb8/2008-10-06_1235.png" width="668" height="427" border="0" /></a></htm>

===Inspect the time-serie results===
*Click on the HDF analysis mode icon, then double-click on any new .srh file, which is a time serie result from the model that can be opened with the [[Time Series Editor]] program that comes bundled with the MOHID suite.
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/1ea6957c-2987-4d63-8653-ce588de76235/2008-10-06_1706.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/1ea6957c-2987-4d63-8653-ce588de76235/2008-10-06_1706.png" width="467" height="163" border="0" /></a></htm>

*Select ''elevation'' then click on ''Ok''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/600af226-0e1e-49c9-b2a5-730d3ab427f2/2008-10-06_1912.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/600af226-0e1e-49c9-b2a5-730d3ab427f2/2008-10-06_1912.png" width="400" height="425" border="0" /></a></htm>

*Select the .srh file present, then click on ''Draw Chart''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/1ea30144-725d-4ecb-a553-eb63d822d828/2008-10-06_1913.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/1ea30144-725d-4ecb-a553-eb63d822d828/2008-10-06_1913.png" width="544" height="407" border="0" /></a></htm>

*Inspect and admire the plotted time serie results :)
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/9ca0ca52-6ba6-4e9a-a709-c43156a30358/2008-10-06_1915.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/9ca0ca52-6ba6-4e9a-a709-c43156a30358/2008-10-06_1915.png" width="576" height="361" border="0" /></a></htm>

==Next steps==
*[[How to create discharges in MOHID]]
*[[How to use the Blumberg-Kantha radiation method]]

==Previous steps==
*[[How_to_create_a_model_gridded_bathymetry%3F|How to create a model gridded bathymetry?]]
*[[How_to_generate_tide_for_Mohid%3F|How to generate tide for Mohid?]]
*[[How_to_configure_a_2D_model_forced_with_tide_with_MOHID|How to configure a MOHID 2D simulation with tide?]]

==About the screen capturing tool==
The screen capturing tool used for this tutorial was the [http://www.jingproject.com/ Jing Project].

[[Category:Graphical User Interfaces]]
[[Category:Help]]
[[Category:Mohid Water]]
[[Category:Exercises]]
[[Category:Example]]
[[Category:Tools]]
[[Category:How To]]

SmoothBatimNesting

2008-11-04T12:37:38Z

192.168.20.177:

[[Image:SmoothBathimNesting.gif|300px|thumb|Animation consisting of three frames showing respectively i) the father bathymetry, ii) the son bathym, iii) and the interpolated bathym.]]
This program creates a new sub-model bathimetry to allow a smooth transition in the boundary between the coarser model and the high resolution model. See also [[SmoothBatimCoefs]].

== Quick start ==
#Create the father and son bathymetries (you may use [[Mohid GIS]]).
#Create the SmoothCoeficients [[Grid Data | griddata file]] (you may use [[SmoothBatimCoefs]]).
#Create and edit the options ''SmoothBatimNesting.dat'' file and save it in the same path as the executable.
#Run the executable.

== Options file ==
Here's what the options file ''SmoothBatimNesting.dat'' looks like:
FATHER_BATIM : ..\..\WestIberiaTide\GridData.dat
SON_BATIM : ..\GridData_2.dat
SMOOTH_COEF : SmoothCoef.dat
NEW_SON_BATIM : SmoothData.dat

== Smoothing algorithm ==
Let it be <math>X \in \mathcal{F}\equiv\left\{F,\,S,\,I\right\}</math>, as an element of the father, the son and the interpolated bathymetries discrete fields. Let it be <math>I_X : \mathbb{N}^2 \longrightarrow \mathbb{R}^2 </math> as the respective index mapping function. Let it be <math> X^{\prime}: \mathbb{R}^2 \longrightarrow \mathbb{R}</math>, a continuous map, so that <math>X \equiv X^\prime\circ I_X,\;\forall X \in \mathcal{F}</math>. Let <math>r_X \subset \mathbb{R}^2</math> define the work domain of <math>X^\prime \in \mathcal{F}^\prime</math>. In particular, <math>X^\prime</math> verifies <math>X^\prime(\overline{r_X})\equiv 0</math>. The son grid is the same as the interpolated grid, meaning <math>I_S = I_I</math>. However, the father field is completely independent from the other fields, meaning that <math>r_{FS}\equiv\left(r_F \cap r_S\right) \subseteq \mathbb{R}^2</math>. The smoothing algorithm is a simple linear interpolation of the father and son fields:
:<math>I^\prime = \left(1 - C^\prime\right) F^\prime + C^\prime\,S^\prime</math>
where the smoothing coefficient is given by <math>C^\prime: \mathbb{R}^2 \longrightarrow \left[0\;1\right]</math>. Thus, the smoothing coefficient gridded counterpart <math>C</math> is defined; and its index mapping function <math>I_C</math> is equal to the son's; meaning <math>I_C = I_S</math>. Let us define the grid <math>G \subseteq \mathbb{N}^2</math> such that <math>I_S(G)\subseteq r_S</math> and <math>I_S(G)\rightarrow r_S</math>. Thus the smoothing coefficient <math>C</math> needs can be defined in <math> G </math>. Concretely speaking, <math>G \mapsto (I_S(G),C(I_S(G)))</math> is the smoothing coefficient's [[Grid Data]] file described above, thus it leaves to the modeller the choice of the smoothing coefficient field.

=== Implementation ===
Let us define a collection of four-vertices polygons taken from the father grid:
:<math>\begin{matrix} V : & \mathbb{N}^2 \longrightarrow \mathbb{R}^8 \\ & \left(i,\,j\right) \mapsto (I_{F\;i\,j},\,I_{F\;i+1\,j},\,I_{F\;i\,j+1},\,I_{F\;i+1\,j+1})\end{matrix} </math>
where <math>D\left(V_{i\,j}\right)\subset \mathbb{R}^2</math> is the subdomain defined by the vertices of <math>V_{i\,j}</math>.
Let us define an auxiliary grid of the son grid given by:
:<math>\forall\; _{ij} \in \mathbb{N}^2,\;\tilde{I}_{S\;i\,j}=\frac{1}{4}\left(I_{S\;i\,j}+I_{S\;i+1\,j}+I_{S\;i\,j+1} +I_{S\;i+1\,j+1}\right)</math>.
Let us define a new mapping into a subset of <math>F</math>'s image:
:\<math>\forall\;_{i\,j} \in \mathbb{N}^2\quad \exists !\;_{u\,v} \in \mathbb{N}^2\; :\quad \tilde{I}_{S\;i\,j} \in D(V_{u\,v}) \wedge \tilde{F}_{i\,j}=F_{u\,v} </math>.
Here's the implemented smoothing algorithm:
:<math>I_{i\,j} = \left(1 - C_{i\,j}\right) \tilde{F}_{i\,j} + C_{i\,j}\,S_{i\,j}</math>.

== Test image ==
[[Image:SmoothBathimNesting.gif|540px|thumb|center|Animation consisting of three frames showing respectively i) the father bathymetry, ii) the son bathym, iii) and the interpolated bathym.]]

[[Category:Tools]]

How to configure a 2D model forced with tide with MOHID

2008-10-31T17:22:08Z

192.168.20.177: /* Step 5 - Inspect the results */

Before you start creating your own simulation, you may want to create a [[How_to_create_a_model_gridded_bathymetry%3F|bathymetry]] and [[How_to_generate_tide_for_Mohid%3F|tidal gauges]] first.

==Step 1 - Create a new mohid GUI project==
*Create a new [[Mohid GUI]] project.

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/06b8d3f5-6b83-4ce7-a5ed-e9779dcad6b5/2008-10-03_1031.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/06b8d3f5-6b83-4ce7-a5ed-e9779dcad6b5/2008-10-03_1031.png" width="304" height="208" border="0" /></a></htm>

*Name the project and select a location

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cca7b5ec-5944-4b1c-a6f7-d0a6a0a31d12/2008-10-03_1033.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cca7b5ec-5944-4b1c-a6f7-d0a6a0a31d12/2008-10-03_1033.png" width="408" height="224" border="0" /></a></htm>

==Step 2 - Insert a new simulation and a new run==
*Right-click and select Insert Simulation

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/f515d76f-6cf2-4f9f-9dd0-9b262d68c95c/2008-10-03_1036.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/f515d76f-6cf2-4f9f-9dd0-9b262d68c95c/2008-10-03_1036.png" width="380" height="199" border="0" /></a></htm>

*Name the simulation, browse and select a bathymetry file, browse and select a tidal gauge data

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png" width="646" height="354" border="0" /></a></htm>

*Right-click on the simulation and select ''New Run''

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/77dc0705-8d6d-4ac9-ba05-39100a6f3297/2008-10-03_1307.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/77dc0705-8d6d-4ac9-ba05-39100a6f3297/2008-10-03_1307.png" width="421" height="182" border="0" /></a></htm>

*Edit at will the start date, the end date and the simulation time-step, then click ''Ok''

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/581eedf9-ff18-4518-9a26-91f7a2c16802/2008-10-03_1309.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/581eedf9-ff18-4518-9a26-91f7a2c16802/2008-10-03_1309.png" width="384" height="296" border="0" /></a></htm>

In order to choose an adequate time-step, <mathtex>\Delta t</mathtex>, we recommend to aim to a 1D [http://en.wikipedia.org/wiki/Courant_number Courant number] of 15; <mathtex>Cr = c \frac{\Delta t}{\Delta x}</mathtex>. In estuarine and shelf waters, you may estimate the system maximum velocity, <mathtex>c</mathtex>, with
<mathtex>c = \sqrt{g\,H} </mathtex>
where <mathtex>H</mathtex> is the maximum depth of your domain and <mathtex>g</mathtex> is local gravitational field (approximately worth 10 m/s2). For example, with a 200 m resolution domain where maximum depth is 400 m, the approximate time step would be around 50 s.

==Step 3 - Configure the modules==
To configure the modules simply double-click on the module icon in the GUI.

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/00740582-0cc8-4ebb-9756-aa073c6eb6a6/2008-10-06_1057.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/00740582-0cc8-4ebb-9756-aa073c6eb6a6/2008-10-06_1057.png" width="656" height="208" border="0" /></a></htm>

Warning: the configuration files are made of a list pairs of keywords and values. '''Only whitespaces are admitted.''' Any tabulation will yield in error during the reading of the keywords.

===[[Module Model]]===
The module model determines the start and end times, as well as the model's time-step. It is probably already configured and should look like this:

START : 2008 10 28 12 0 0
END : 2008 10 31 12 0 0
DT : 50.
VARIABLEDT : 0
GMTREFERENCE : 0
SPLITTING : Double_Splitting

===[[Module Atmosphere]]===
The module atmosphere configures the atmospheric forcing such as wind, solar radiation, latent and sensible heat sea-air exchange, infrared radiation.
In this test-case, we have no atmospheric forcing, thus the file should be left in blank.

===[[Module Geometry]]===
The module geometry describes the vertical discretization of the domain. In this test-case we have a single vertical layer, since the model is 2D.

MINIMUMDEPTH : 0.1000

<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 1
LAYERTHICKNESS : 1.0000
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
<enddomain>

===[[Module InterfaceWaterAir]]===
This module parameterizes the exchanges of momentum, radiation, heat and salt between the atmosphere and the water. In this case, we simply need to define the surface rugosity.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

===[[Module InterfaceSedimentWater]]===
This module parameterizes the exchanges of momentum, mass and heat between the sediments and the water. In this case, we simply need to define the bottom rugosity.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

===[[Module Hydrodynamic]]===
This module parameterizes the numerical model solving the advection-diffusion equations of momentum combined with the continuity equation. It includes also boundary conditions definitions, as well as initialization conditions. Finally, assimilation schemes of U, V or water level. The momentum equations are also modularized, in the sense that each of its components may, or may not, be deactivated.

In this case we are simply choosing a TVD spatial numerical scheme, while adding the Coriolis force to the momentum equations. Since the model is 2D and has homogeneous density, the baroclinic term in the pressure gradient is deactivated, for performance sake. The model starts at rest and has the water level forced with tide at the open-boundaries. The model outputs results every 3 hours. Furthermore it will also output residual (averaged) hydrodynamic results and a domain-integrated energy time-serie.

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4

BAROCLINIC : 0

CORIOLIS : 1

TIDE : 1

OUTPUT_TIME : 0. 10800.

RESIDUAL : 1
ENERGY : 1

===[[Module Turbulence]]===
The module Turbulence configures how the horizontal and vertical sub-grid scale turbulent viscosities are calculated. In this case we opt for constant sub-grid scale viscosities.

VISCOSITY_V : 0.0010
VISCOSITY_H : 20

===[[Module WaterProperties]]===
The module Waterproperties applies the advection-diffusion equation to any eulerian tracer. It could be the salinity, the temperature, or any other property that is advected and diffused in the water. In this case we have a homogeneous density, thus we don't need to calculate the density field, thus there's no need to transport salinity or temperature or any other waterproperty for that matter. Hence we leave a blank file in the module Waterproperties in this test-case.

==Step 4 - Running the model==
If all is correctly configured, and all the input files are double-checked, we can hopefully start running our model!

*Select ''Tools'' from menu, then ''Launch Mohid...''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/6e5c5742-0f44-4538-8d57-9b25886c2acd/2008-10-06_1228.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/6e5c5742-0f44-4538-8d57-9b25886c2acd/2008-10-06_1228.png" width="785" height="231" border="0" /></a></htm>

*Select the ''Run_1'', then select ''Run Mohid'', then select ''Launch after Ok'', then click on ''Ok''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a4180c38-199d-48e8-8e40-e5d0684c0785/2008-10-06_1230.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a4180c38-199d-48e8-8e40-e5d0684c0785/2008-10-06_1230.png" width="616" height="617" border="0" /></a></htm>

*Supervise the screen-outputs to check for any error, or to simply read the estimated end time of simulation
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/f536ea29-1ca2-4929-8dd4-3660f5a5bdb8/2008-10-06_1235.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/f536ea29-1ca2-4929-8dd4-3660f5a5bdb8/2008-10-06_1235.png" width="668" height="427" border="0" /></a></htm>

==Step 5 - Inspect the results==
Once the model has finished running, (or while the model is running, after it has created a few HDF5 outputs), you will want to switch in analysis mode and graphically inspect the results to see if all went well (or is going well). We will proceed to visualize the instantaneous velocity as a vector field, and the instantaneous water level as a colormap field. The proceedings are exactly the same for any other variables.

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/668b5840-a5eb-4763-adf4-91031475df86/2008-10-06_1248.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/668b5840-a5eb-4763-adf4-91031475df86/2008-10-06_1248.png" width="725" height="140" border="0" /></a></htm>

* Click on HDF file, then click on Grid HDF group
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/62494ac5-780c-40bf-a04d-117fab259c9a/2008-10-06_1252.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/62494ac5-780c-40bf-a04d-117fab259c9a/2008-10-06_1252.png" width="633" height="428" border="0" /></a></htm>

*Map the GridY, GridX, VerticalZ and Mapping with the Group items Latitude, Longitude, VerticalZ and OpenPoints, respectively.
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a6311453-fd93-4ff4-8023-d1538e263330/2008-10-31_1715.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a6311453-fd93-4ff4-8023-d1538e263330/2008-10-31_1715.png" width="633" height="428" border="0" /></a></htm>

*Map the time HDF Group to the Time selection button
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/1e8c0033-8310-407d-8806-84063acedda8/2008-10-06_1354.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/1e8c0033-8310-407d-8806-84063acedda8/2008-10-06_1354.png" width="633" height="428" border="0" /></a></htm>

*Map the Velocity U, Velocity V and Water level HDF results group's items to the Vector X, Vector Y and Color selection buttons, respectively
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/5d04934d-1e86-4423-9d4e-9911b1de98fa/2008-10-06_1407.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/5d04934d-1e86-4423-9d4e-9911b1de98fa/2008-10-06_1407.png" width="633" height="428" border="0" /></a></htm>

*From the ''Action menu'', select ''Run OpenGL''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cd534e3b-85ce-4360-8d41-ced22a250d14/2008-10-06_1412.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cd534e3b-85ce-4360-8d41-ced22a250d14/2008-10-06_1412.png" width="380" height="162" border="0" /></a></htm>

*Select ''settings''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/85dfbcf2-0953-440f-ab04-dda08d871d05/2008-10-06_1417.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/85dfbcf2-0953-440f-ab04-dda08d871d05/2008-10-06_1417.png" width="167" height="254" border="0" /></a></htm>

*Select ''Color''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/09e8730a-97bc-4c9a-9f05-4845044dadc3/2008-10-06_1419.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/09e8730a-97bc-4c9a-9f05-4845044dadc3/2008-10-06_1419.png" width="302" height="465" border="0" /></a></htm>

*Define the minimum water level (m) and the maximum water level (m). Then click on ''Ok''.
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a6cc16ef-6a55-46e9-9087-0f91b5434cd9/2008-10-06_1433.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a6cc16ef-6a55-46e9-9087-0f91b5434cd9/2008-10-06_1433.png" width="302" height="465" border="0" /></a></htm>

*Select ''Vectors''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/e3980360-d91a-40fb-9f3d-494b69f3803e/2008-10-06_1421.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/e3980360-d91a-40fb-9f3d-494b69f3803e/2008-10-06_1421.png" width="302" height="465" border="0" /></a></htm>

*Define the vector ''Scale'' to 0.2 and the vector stepping along X and along Y to 6. Then click on ''Ok''.
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/38b5013e-19c3-484c-8f3d-b61bc6d6d702/2008-10-06_1434.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/38b5013e-19c3-484c-8f3d-b61bc6d6d702/2008-10-06_1434.png" width="272" height="360" border="0" /></a></htm>

*Render the results, frame by frame
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/af97e06b-aea2-468a-9a64-9de3fd4d290a/2008-10-06_1455.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/af97e06b-aea2-468a-9a64-9de3fd4d290a/2008-10-06_1455.png" width="619" height="463" border="0" /></a></htm>

If all went well, you should see results with patterns and values as expected for the domain. Now you can try to add time series, or to improve the open boundary conditions ...

==Next steps==
*[[How to create MOHID timeseries outputs]]
*[[How to create discharges in MOHID]]
*[[How to use the Blumberg-Kantha radiation method]]

==Previous steps==
*[[How_to_create_a_model_gridded_bathymetry%3F|How to create a model gridded bathymetry?]]
*[[How_to_generate_tide_for_Mohid%3F|How to generate tide for Mohid?]]

==About the screen capturing tool==
The screen capturing tool used for this tutorial was the [http://www.jingproject.com/ Jing Project].

[[Category:Graphical User Interfaces]]
[[Category:Help]]
[[Category:Mohid Water]]
[[Category:Exercises]]
[[Category:Example]]
[[Category:Tools]]
[[Category:How To]]

How to create discharges in MOHID

2008-10-31T17:19:42Z

192.168.20.177: /* Inspect the results */

In this tutorial we will continue to work on the simulation we built on the [[How_to_configure_a_2D_model_forced_with_tide_with_MOHID|previous tutorial]] and we will show how to add an instantaneous discharge and a gradual discharge in the model, by setting up and configuring the [[Module Discharges]].

==Step 1 - Identify the discharge location==
Right now we're going to identify exactly what are the discharges locations. We want to simulate an accidental instantaneous discharge of a passive tracer and a continuous discharge as a function of time nearby a dam.

===In Google Earth===
[[Google_Earth#Configure_Google_Earth|Make sure you have Google Earth correctly configured!!]]

*Select the placemark icon, give the discharge a name, and give it a position
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/7a8d87b3-eb5b-46aa-96d0-3b6ef894828d/2008-10-07_1210.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/7a8d87b3-eb5b-46aa-96d0-3b6ef894828d/2008-10-07_1210.png" width="650" height="436" border="0" /></a></htm>

Repeat the procedure, for the point nearby the dam.

*Save the location by right-clicking on them, and selecting ''save as...''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/bcd3dd5f-869e-41a2-b89f-fc3e6fbbe64b/2008-10-07_1421.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/bcd3dd5f-869e-41a2-b89f-fc3e6fbbe64b/2008-10-07_1421.png" width="326" height="273" border="0" /></a></htm>

*Select a folder, choose a filename, select ''kml'' filetype, click on ''save'' button
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/5c224dd7-1089-433b-999c-2c838b7a94ef/2008-10-07_1423.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/5c224dd7-1089-433b-999c-2c838b7a94ef/2008-10-07_1423.png" width="563" height="412" border="0" /></a></htm>

===In Mohid GIS===

====Convert from kml to xyz====
*Get the [http://www.mohid.com/hydrogroup/data_sources/kml2mohid.exe kml2mohid.exe] program and save it next to the kml file, in the same folder, then type from the command line shell:
> [http://www.mohid.com/hydrogroup/data_sources/kml2mohid.exe kml2mohid.exe] discharges.kml
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/feff4f5b-a082-4822-8f8a-9c9ba0f291bf/2008-10-07_1428.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/feff4f5b-a082-4822-8f8a-9c9ba0f291bf/2008-10-07_1428.png" width="532" height="167" border="0" /></a></htm>

====Add data as a points GIS layer, identify corresponding cell grids====
*Open the Mohid GIS, and open the GIS project we left before:
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/61ce1989-e762-4378-80ad-0d0d33bce34d/2008-10-07_1453.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/61ce1989-e762-4378-80ad-0d0d33bce34d/2008-10-07_1453.png" width="220" height="227" border="0" /></a></htm>

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/40b33990-b40d-4130-a2b6-de731493dca0/2008-10-07_1458.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/40b33990-b40d-4130-a2b6-de731493dca0/2008-10-07_1458.png" width="459" height="366" border="0" /></a></htm>

*Add new data item from the ''Data Items menu''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/0f6a14a1-4606-49b2-a42b-bb8673bc4119/2008-10-07_1502.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/0f6a14a1-4606-49b2-a42b-bb8673bc4119/2008-10-07_1502.png" width="256" height="211" border="0" /></a></htm>

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/2ce6326b-71e2-409b-8d78-2a478fb46011/2008-10-07_1506.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/2ce6326b-71e2-409b-8d78-2a478fb46011/2008-10-07_1506.png" width="563" height="412" border="0" /></a></htm>

*Drag'n drop the xyz points data layer to the top, then right-click it and select ''Properties''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/ebb9ebf0-e343-4f53-9464-59f0f267571c/2008-10-07_1519.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/ebb9ebf0-e343-4f53-9464-59f0f267571c/2008-10-07_1519.png" width="329" height="165" border="0" /></a></htm>

*Set size to 6, then select ''Pick Color''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/8a2fd395-9ac0-468a-a72e-d7b4de394d2c/2008-10-07_1522.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/8a2fd395-9ac0-468a-a72e-d7b4de394d2c/2008-10-07_1522.png" width="364" height="156" border="0" /></a></htm>

*Pick a bright color, then click on ''Ok'', twice
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/de8f8f1c-0905-4c22-a3c4-aff4125aeee9/2008-10-07_1524.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/de8f8f1c-0905-4c22-a3c4-aff4125aeee9/2008-10-07_1524.png" width="348" height="349" border="0" /></a></htm>

*Check the grid layer, and make sure that it is on top of the grid data layer, so it is displayed in the view area of the MOHID GIS
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/08418f4b-d051-4753-adce-8bcef1c644b6/2008-10-07_1528.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/08418f4b-d051-4753-adce-8bcef1c644b6/2008-10-07_1528.png" width="317" height="84" border="0" /></a></htm>

*Select the ''area information'' icon, then select a small area containing the discharge point. Then read the I and J grid coordinates for later usage. Repeat this process for every discharge point.
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/26cbaf60-6738-4f88-bea9-ff84d917ee55/2008-10-07_1543.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/26cbaf60-6738-4f88-bea9-ff84d917ee55/2008-10-07_1543.png" width="365" height="414" border="0" /></a></htm>

==Step 2 - Create a time-serie simulating the discharge==
In order to create a time-serie that simulates a continuous discharge (to simulate, say, a river), you must open a new text file and format the data accordingly with this sample

TIME_UNITS : DAYS
SERIE_INITIAL_DATA : 2008 10 27 0 0 0

Time Flow T S
days m3/s C psu
1 2 3 4
<BeginTimeSerie>
0 1520.00 11.4 0.0
1 1440.00 11.3 0.0
2 1340.00 11.2 0.0
3 1290.00 11.2 0.0
4 1270.00 11.1 0.0
5 1200.00 11.1 0.0
6 1160.00 11.0 0.0
7 1190.00 10.9 0.0
8 1320.00 10.9 0.0
<EndTimeSerie>

Then, once you have created a time-serie with the flow discharge, you simply save it in your [[MohidWater]] project ''GeneralData'' folder.

Notes: the time containing column should be composed of integers. Thus, adjust the TIME_UNITS parameter accordingly. The flow column is mandatory, whereas the T
(temperature) and S (salinity) columns in the example are optional.

==Step 3 - Configure the Discharges module and run MohidWater==

===Configure the [[Module Discharges]]===

*Open the project from the [[How_to_configure_a_2D_model_forced_with_tide_with_MOHID|last tutorial]]
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a51a3fd4-4a4f-4351-bc4e-c50de4058182/2008-10-07_1652.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a51a3fd4-4a4f-4351-bc4e-c50de4058182/2008-10-07_1652.png" width="224" height="116" border="0" /></a></htm>

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/eb9ffe1b-7980-432a-9324-5627f50e6772/2008-10-07_1658.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/eb9ffe1b-7980-432a-9324-5627f50e6772/2008-10-07_1658.png" width="563" height="412" border="0" /></a></htm>

*Right-click the ''run_1'' and select ''Properties''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/40c98f70-e478-44c5-b857-7b39a88dd761/2008-10-07_1700.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/40c98f70-e478-44c5-b857-7b39a88dd761/2008-10-07_1700.png" width="280" height="201" border="0" /></a></htm>

*Select in the ''associated modules'' the ''module discharges''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/681ffdee-efd9-4ba4-9cfc-6cb2c28d5e15/2008-10-07_1721.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/681ffdee-efd9-4ba4-9cfc-6cb2c28d5e15/2008-10-07_1721.png" width="357" height="312" border="0" /></a></htm>

*Edit the [[Module Discharges]] according to the sample below, then save it. Notice we're adding two discharges: a continuous discharge, and an accidental discharge. Notice also that we're adding a single property, salinity. Properties are optional; there could be several as well as there could be none.

<begindischarge>
NAME : Dam discharge
DESCRIPTION : Daily timeserie for the year 2008
I_CELL : 280
J_CELL : 222
DISCHARGE_UNIFORM : 1
DATA_BASE_FILE : D:\Aplica\Senegal-Test\GeneralData\Discharges\river_discharge_sample2.srw
FLOW_COLUMN : 2
TIME_SERIE_COLUMN : 1

<<beginproperty>>
NAME : salinity
UNITS : psu
DESCRIPTION : freshwater accidental discharge
CONSTANT_CONC : 1
DEFAULTVALUE : 0.01
<<endproperty>>

<enddischarge>

<begindischarge>
NAME : Accidental discharge
DESCRIPTION : Daily timeserie for the year 2008
I_CELL : 131
J_CELL : 165
DISCHARGE_UNIFORM : 1
DATA_BASE_FILE : D:\Aplica\Senegal-Test\GeneralData\Discharges\river_discharge_sample2.srw
FLOW_COLUMN : 2
TIME_SERIE_COLUMN : 1

<<beginproperty>>
NAME : salinity
UNITS : psu
DESCRIPTION : freshwater accidental discharge
CONSTANT_CONC : 1
DEFAULTVALUE : 0.01
<<endproperty>>

<enddischarge>

*Edit the [[Module Hydrodynamic]], add the following line, then save it
WATER_DISCHARGES : 1

*If there's a property in the discharge (in occurence, there's salinity), then edit the [[Module WaterProperties]], and add the following lines, then save it. The single most relevant pair parameter/value for discharges in the module WaterProperties is '''DISCHARGES : 1'''.

''Notes: Relatively to the project from the [[How_to_configure_a_2D_model_forced_with_tide_with_MOHID|last tutorial]], we're adding the salinity property as a passive tracer. It will be advected with the same advection-diffusion method used for momentum and it will also yield a time serie for the same locations as the hydrodynamic's and it will also results every three hours in another HDF5 file. The initial model salinity will be homogeneous, with its default value.''

OUTPUT_TIME : 0 10800.

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4

TIME_SERIE : 1
TIME_SERIE_LOCATION : D:\Users\Soussou\GeneralData\TimeSeries\StLouisTimeSeries.dat

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : salinity by default is 36
DEFAULTVALUE : 36

ADVECTION_DIFFUSION : 1
OUTPUT_HDF : 1
DISCHARGES : 1

TIME_SERIE : 1
<endproperty>

===Run Mohid and inspect the results===
If all is correctly configured, and all the input files are double-checked, we can hopefully start running our model!

====Run Mohid====
*Select ''Tools'' from menu, then ''Launch Mohid...''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/6e5c5742-0f44-4538-8d57-9b25886c2acd/2008-10-06_1228.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/6e5c5742-0f44-4538-8d57-9b25886c2acd/2008-10-06_1228.png" width="785" height="231" border="0" /></a></htm>

*Select the ''Run_1'', then select ''Run Mohid'', then select ''Launch after Ok'', then click on ''Ok''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a4180c38-199d-48e8-8e40-e5d0684c0785/2008-10-06_1230.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a4180c38-199d-48e8-8e40-e5d0684c0785/2008-10-06_1230.png" width="616" height="617" border="0" /></a></htm>

*Supervise the screen-outputs to check for any error, or to simply read the estimated end time of simulation
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/f536ea29-1ca2-4929-8dd4-3660f5a5bdb8/2008-10-06_1235.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/f536ea29-1ca2-4929-8dd4-3660f5a5bdb8/2008-10-06_1235.png" width="668" height="427" border="0" /></a></htm>

====Inspect the results====

Once the model has finished running, (or while the model is running, after it has created a few HDF5 outputs), you will want to switch in analysis mode and graphically inspect the results to see if all went well (or is going well). We will proceed to visualize the instantaneous velocity as a vector field, and the instantaneous water level as a colormap field. The proceedings are exactly the same for any other variables.

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/668b5840-a5eb-4763-adf4-91031475df86/2008-10-06_1248.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/668b5840-a5eb-4763-adf4-91031475df86/2008-10-06_1248.png" width="725" height="140" border="0" /></a></htm>

* Click on HDF file, then click on Grid HDF group
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/62494ac5-780c-40bf-a04d-117fab259c9a/2008-10-06_1252.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/62494ac5-780c-40bf-a04d-117fab259c9a/2008-10-06_1252.png" width="633" height="428" border="0" /></a></htm>

*Map the GridY, GridX, VerticalZ and Mapping with the Group items Latitude, Longitude, VerticalZ and OpenPoints, respectively.
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a6311453-fd93-4ff4-8023-d1538e263330/2008-10-31_1715.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a6311453-fd93-4ff4-8023-d1538e263330/2008-10-31_1715.png" width="633" height="428" border="0" /></a></htm>

*Map the time HDF Group to the Time selection button
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/1e8c0033-8310-407d-8806-84063acedda8/2008-10-06_1354.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/1e8c0033-8310-407d-8806-84063acedda8/2008-10-06_1354.png" width="633" height="428" border="0" /></a></htm>

*Map the Velocity U, Velocity V and Water level HDF results group's items to the Vector X, Vector Y and Color selection buttons, respectively
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/5d04934d-1e86-4423-9d4e-9911b1de98fa/2008-10-06_1407.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/5d04934d-1e86-4423-9d4e-9911b1de98fa/2008-10-06_1407.png" width="633" height="428" border="0" /></a></htm>

*From the ''Action menu'', select ''Run OpenGL''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cd534e3b-85ce-4360-8d41-ced22a250d14/2008-10-06_1412.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cd534e3b-85ce-4360-8d41-ced22a250d14/2008-10-06_1412.png" width="380" height="162" border="0" /></a></htm>
*Select ''settings''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/85dfbcf2-0953-440f-ab04-dda08d871d05/2008-10-06_1417.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/85dfbcf2-0953-440f-ab04-dda08d871d05/2008-10-06_1417.png" width="167" height="254" border="0" /></a></htm>

*Select ''Color''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/09e8730a-97bc-4c9a-9f05-4845044dadc3/2008-10-06_1419.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/09e8730a-97bc-4c9a-9f05-4845044dadc3/2008-10-06_1419.png" width="302" height="465" border="0" /></a></htm>

*Define the minimum water level (m) and the maximum water level (m). Then click on ''Ok''.
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a6cc16ef-6a55-46e9-9087-0f91b5434cd9/2008-10-06_1433.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a6cc16ef-6a55-46e9-9087-0f91b5434cd9/2008-10-06_1433.png" width="302" height="465" border="0" /></a></htm>

*Select ''Vectors''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/e3980360-d91a-40fb-9f3d-494b69f3803e/2008-10-06_1421.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/e3980360-d91a-40fb-9f3d-494b69f3803e/2008-10-06_1421.png" width="302" height="465" border="0" /></a></htm>

*Define the vector ''Scale'' to 0.2 and the vector stepping along X and along Y to 6. Then click on ''Ok''.
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/38b5013e-19c3-484c-8f3d-b61bc6d6d702/2008-10-06_1434.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/38b5013e-19c3-484c-8f3d-b61bc6d6d702/2008-10-06_1434.png" width="272" height="360" border="0" /></a></htm>

If all went well, you should see results with patterns and values as expected for the domain.

*Here is the result of discharging water in a river
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/e5b5b20b-3fdc-48d8-bfef-90612aec0a19/2008-10-08_1057.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/e5b5b20b-3fdc-48d8-bfef-90612aec0a19/2008-10-08_1057.png" width="507" height="356" border="0" /></a></htm>

*Now, in order to render the results with the salinity map, you need to close the current post-processor rendering
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/d45e6644-21f5-4bbf-8d31-f20011b6876c/2008-10-09_1205.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/d45e6644-21f5-4bbf-8d31-f20011b6876c/2008-10-09_1205.png" width="167" height="254" border="0" /></a></htm>

*delete all the color layer instants of waterlevel,
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/a29f6bbd-1c56-45f8-9fd2-4ba7643fe3de/2008-10-09_1208.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a29f6bbd-1c56-45f8-9fd2-4ba7643fe3de/2008-10-09_1208.png" width="633" height="428" border="0" /></a></htm>

*open the waterproperties hdf5 file,
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/aa6cdde3-5fef-4992-ae56-a4c7d6449b8f/2008-10-09_1211.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/aa6cdde3-5fef-4992-ae56-a4c7d6449b8f/2008-10-09_1211.png" width="184" height="165" border="0" /></a></htm>

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/e5ae6f7a-6ae3-48b8-9de0-f0576843a6fc/2008-10-09_1214.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/e5ae6f7a-6ae3-48b8-9de0-f0576843a6fc/2008-10-09_1214.png" width="563" height="412" border="0" /></a></htm>

*load the salinity property as a color layer,
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/088bdb4e-b673-442f-be8d-2ff9e29db9f3/2008-10-09_1218.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/088bdb4e-b673-442f-be8d-2ff9e29db9f3/2008-10-09_1218.png" width="633" height="428" border="0" /></a></htm>

*re-run in OpenGL mode
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/48d4a2b3-436c-434d-8e2e-542477472af8/2008-10-09_1221.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/48d4a2b3-436c-434d-8e2e-542477472af8/2008-10-09_1221.png" width="205" height="155" border="0" /></a></htm>

*Edit the color layer settings to a minimum of 0 and a maximum of 36.5 (as salinity in this case varies between these extrema).
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/59392676-6cfe-42c3-8472-0c1ce9abb3b5/2008-10-09_1223.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/59392676-6cfe-42c3-8472-0c1ce9abb3b5/2008-10-09_1223.png" width="167" height="254" border="0" /></a></htm>

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/f0f3cf2f-50bd-4165-8428-613640c72646/2008-10-09_1224.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/f0f3cf2f-50bd-4165-8428-613640c72646/2008-10-09_1224.png" width="171" height="126" border="0" /></a></htm>

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/b1284e35-4589-40e5-93f9-45ecca595422/2008-10-09_1225.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/b1284e35-4589-40e5-93f9-45ecca595422/2008-10-09_1225.png" width="272" height="417" border="0" /></a></htm>

*Once you apply with the settings, you can now render each frame and watch the freshwater discharge flow along your simulation. Thus, here is the result of an accidental freshwater discharge
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/5f5e6468-a7ad-4884-9511-b0bd02c5e6f0/2008-10-08_1246.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/5f5e6468-a7ad-4884-9511-b0bd02c5e6f0/2008-10-08_1246.png" width="541" height="345" border="0" /></a></htm>

==Next steps==
*[[How to use the Blumberg-Kantha radiation method]]

==Previous steps==
*[[Software to run Mohid]]
*[[How_to_create_a_model_gridded_bathymetry%3F|How to create a model gridded bathymetry?]]
*[[How_to_generate_tide_for_Mohid%3F|How to generate tide for Mohid?]]
*[[How_to_configure_a_2D_model_forced_with_tide_with_MOHID|How to configure a MOHID 2D simulation with tide?]]
*[[How_to_create_MOHID_timeseries_outputs|How to create MOHID time series outputs?]]

==About the screen capturing tool==
The screen capturing tool used for this tutorial was the [http://www.jingproject.com/ Jing Project].

[[Category:Graphical User Interfaces]]
[[Category:Help]]
[[Category:Mohid Water]]
[[Category:Exercises]]
[[Category:Example]]
[[Category:Tools]]
[[Category:How To]]

Software to run Mohid

2008-10-29T16:40:39Z

192.168.20.177: /* Tutorials */

In order to run Mohid you need the following software

==System requirements==
* Windows XP or Vista
* 1 GB ram (2 GB recommended)
* Hardware graphical accelerator
* 250 MB of free hard-disk space (1 GB or more is recommended)
* Internet access (for documentation and support)

'''WORD OF CAUTION: You need to configure the windows settings so that the decimal separator be a point. For example: 4.1516 is correct but 4,1516 is incorrect. If the separator isn't a point, then importing data files into MOHID GIS may yield errors.'''

'''WORD OF CAUTION2: Google earth must effectuate the points in decimal values as well, instead of the typical degrees, minutes, seconds.'''

==Downloads==
* Register, login, download and install the latest version of the Mohid package [http://www.mohid.com/MembersArea/index.asp here]. It will include:
** [[MohidWater]], [[Mohid GIS|GIS]], [[Mohid GUI|GUI]], [[Mohid PostProcessor]], [[Mohid Time Series Editor]]

* Download and install [http://earth.google.com/ Google earth].
* Download and store the [http://www.mohid.com/hydrogroup/data_sources/kml2mohid.exe kml2mohid.exe] program.

* Download and uncompress the [http://www.mohid.com/hydrogroup/data_sources/convert.zip ConvertToXyz] program.
* Download and store the [http://www.ngdc.noaa.gov/mgg/global/etopo2.html ETOPO2V2] bathymetry data in '''raw binary format''', '''cell centered''', '''little-endian'''.

*Download and uncompress the [http://maretec.mohid.com/PublicData/products/Software/Mohid-Tide_v0.4.zip Mohid-Tide] program.
* Download and store the [http://www.legos.obs-mip.fr/en/share/soa/cgi/getarc/v0.0/index.pl.cgi?contexte=SOA&donnees=maree&produit=modele_fes Fes2004] tide solution. '''Data access''', '''fes2004''', '''tide''', '''tide.fes2004.nce'''.

==Tutorials==
Once you downloaded and installed everything above, you can read the following tutorials. Note that they are in the recommended order:

#[[How_to_create_a_model_gridded_bathymetry%3F|How to create a model gridded bathymetry in Mohid?]]
#[[How_to_generate_tide_for_Mohid%3F|How to generate tide for Mohid?]]
#[[How_to_configure_a_2D_model_forced_with_tide_with_MOHID|How to configure a 2D model with Mohid?]]
#[[How_to_create_MOHID_timeseries_outputs|How to create MOHID timeseries outputs?]]
#[[How_to_create_discharges_in_MOHID|How to create discharges in MOHID?]]

[[Category:Tools]]
[[Category:How To]]

How to create a model gridded bathymetry?

2008-10-29T16:37:44Z

192.168.20.177: /* Previous steps */

How to create a model gridded bathymetry?

==Step 1 - Extract Ocean bathymetry data from ETOPO 2'==

=== Google Earth===
[[Google_Earth#Configure_Google_Earth|Make sure you have Google Earth correctly configured!!]]
*Define the ETOPO 2' extraction domain limits
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/091fbeaa-1c4a-445a-a501-970eec891e3c/2008-09-25_1729.png"></div></htm>

=== Etopo data file ===
*The internet address where to download the data is http://www.ngdc.noaa.gov/mgg/global/global.html; Download the ETOPO2V2 raw binary data to use with the [[ConvertToXYZ]] program.
*The intranet address is ''\\kepler\DataCenter1\DataCenter\DadosBase\Oceanografia\Batimetria\Etopo\Etopo2\Data''
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/c8db4980-a1dd-4215-b82f-d61475fc9169/2008-09-25_1734.png"></div></htm>

A sample configuration file '''ConvertToXYZ.dat''' is:

<begin_window>
FILE_TYPE : 2
INPUT_FILENAME : \\kepler\DataCenter1\DataCenter\DadosBase\Oceanografia\Batimetria\Etopo\Etopo2\Data\etopo2.dat
OUTPUT_FILENAME : SLouisCoast_ETOPO2.xyz
TOP : 17
BOTTOM : 14
LEFT : -18
RIGHT : -14
MAXIMUM : 1
MINIMUM : -9999
WRITE_AS_BATHYMETRY : 1
CONVERT_TO_HDF5 : 0
<end_window>

<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/2c6039ac-06d7-4190-a22b-e0bb3b1cc69f/2008-09-25_1738.png"></div></htm>

<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/eccf1818-ac75-4528-b819-a059a410fdc2/2008-09-25_1755.png"></div></htm>

*Sample of XYZ data extracted from ETOPO 2'. How the bathymetry XYZ file should look like.
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/2ec3a00d-857b-4116-8d2d-c0f7116e325d/2008-09-25_1812.png"></div></htm>

=== MOHID GIS ===

*Open new project in Mohid GIS
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/be419508-098a-402f-8c0a-a1f3e1bae1d6/2008-09-25_1758.png"></div></htm>

*Give name and location to new project, then save
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/7ceffc83-b6ae-4bba-95cd-d8cea4b7434b/2008-09-25_1759.png"></div></htm>

*Add new data item
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/2711bd08-8603-410d-bdee-b5a4a47ac7e9/2008-09-25_1801.png"></div></htm>

*Select data item and open
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/82f96607-836d-4a02-9327-966830d2f8d1/2008-09-25_1803.png"></div></htm>

*Right-click data, zoom select, right-click, properties
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/2c754098-c707-4bd3-80f6-cbb0fc595df4/2008-09-25_1805.png"></div></htm>

*Click on settings to set the colar palette and color range
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/b9d0d1ac-5387-4260-9ac0-687282513d1e/2008-09-25_1817.png"></div></htm>

*Choose min depth (negative if above sea level), max depth and color palette
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/a0295c41-2935-4a63-a69f-7765c0b0ecaa/2008-09-25_1820.png"></div></htm>

*IMPORTANT: Click ''Save All'' from the ''Data Items'' menu. Otherwise you risk to loose all your work!
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/fa43bb14-6b40-41c5-8fcb-7f8427e8c905/2008-09-25_1837.png"></div></htm>

== Step 2 - Create a coast line ==

=== Create coast line in Google Earth ===

*Create a polygon shaped like the line of the coast
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/6ea1a270-cb13-4060-9084-ab8717058c2e/2008-09-25_2015.png"></div></htm>

*Right-click on polygon, then "save as"
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/3320aa3b-f3c0-4bf9-a8a0-573b1c4dd2ce/2008-09-25_1832.png"></div></htm>

*Save the file in Kml format (NOT in Kmz format)
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/ee02f2ac-7d98-455a-8109-dfd34b64ffe1/2008-09-25_1834.png"></div></htm>

=== Run Kml2mohid ===

*Get the [[Kml2Mohid]] program, edit a batch file, and run the program
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/4ed24f90-dd2b-49bb-8a12-4c94c4212ab4/2008-09-25_1847.png"></div></htm>

*Successfully run [[Kml2Mohid]] program.
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/629db22c-73c4-4ef8-81b4-b73f94f0216a/2008-09-25_1852.png"></div></htm>

*Sample polygon (.xy) file
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/f775b5a4-096d-4c4c-b7a1-1912a64d9834/2008-09-25_1854.png"></div></htm>

=== Import coastline polygon in Mohid ===

*Click ''Data Items'' menu, then select ''Add Data Items...''
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf323931-065d-413d-861b-d0b629894908/2008-09-25_1858.png"></div></htm>

*Select folder, select polygon file type, select file and click open
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/034730fe-19e5-4f29-bfbc-aee611411d29/2008-09-25_1901.png"></div></htm>

*Right-click polygon data, then select ''Properties''
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/08500fa8-23c6-48b0-bd03-a03c0dc9e025/2008-09-25_1905.png"></div></htm>

*Click on settings
<htm><div style="width:100%;text-align:center"><img width="70%" src="<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/8e606f02-8ad9-46ab-b2eb-82d72164b322/2008-09-25_1907.png"></div></htm>

*Select ''Constant'' and choose a color
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/7dbec8eb-e7e3-45ef-b785-58035f416da1/2008-09-25_1908.png"></div></htm>

*Very important: ''Save All'' from the ''Data Items'' menu
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/8b3323bb-0fef-47b8-afa5-acabdc5cf8dd/2008-09-25_1957.png"></div></htm>

*General look of ETOPO points data layer and coastline polygon layer
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/2173549d-71f1-42a5-a79b-4609575e2baa/2008-09-25_2020.png"></div></htm>

== Step 3 - Create the model domain regular grid in MOHID GIS ==

=== Define the grid ===

*Choose bottom-left origin for the model domain
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/14187bbb-1bb9-4f88-9cdc-c24ea63fc7bc/2008-09-25_2032.png"></div></htm>

*Choose model domain grid resolution with [[Google Earth]]
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/bd31b051-8358-4bce-8408-3861318924b3/2008-09-25_1942.png"></div></htm>

*Click on ''Data Item'' menu, then select ''New Data Item''
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/caf030f5-a5d3-45cb-80ea-08bc2f9e2b39/2008-09-25_1917.png"></div></htm>

*Select ''Simple Grid'', then click on ''Browse''
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/1bbe5e5f-021c-4e4c-b308-7891c341223b/2008-09-25_1920.png"></div></htm>

*Give name, select ''Grid file'' as file type, click on ''Save''
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/65818878-26de-493d-b0fa-34282d0c9fa6/2008-09-25_1921.png"></div></htm>

*Click ''Ok''
<htm><div style="width:100%;text-align:center"><img width="70%" src="<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/5881fb84-70d9-4fae-b857-a8e7ae15f315/2008-09-25_1924.png"></div></htm>

*Right-click the Grid layer, then select ''Properties'' from the menu
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/4fa42c28-082c-421a-aae1-98615bb100e9/2008-09-25_1925.png"></div></htm>

*Define origin, define resolution, define grid size, choose ''Simple Geographic'' coordinates type (and NOT ''Geographic'' as seen in the figure. CAUTION!)
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/8ee49234-c066-47cd-b82b-47f52bc5a465/2008-09-25_1930.png"></div></htm>

*Very important: ''Save All'' from the ''Data Items'' menu
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/8b3323bb-0fef-47b8-afa5-acabdc5cf8dd/2008-09-25_1957.png"></div></htm>

*General look of a bathymetry points data from ETOPO, a coastline and land polygon, and a model domain grid
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/b7936c41-8f29-4838-9993-bdff4cb7abad
/2008-09-25_1938.png"></div></htm>

=== Create Digital Terrain from Mohid GIS===

*Click on menu ''Tools'', select ''Create Digital Terrain ...''
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/26403c0a-f816-4b63-bc0c-404821742e3b/2008-09-25_1947.png"></div></htm>

*Select grid layer, data points layers, land polygon layers. Then click ''Browse''
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/17deee31-bb92-4934-8e6b-1572057c6071/2008-09-25_1949.png"></div></htm>

*Choose ''Options'' menu, select ''Triangulation'', select ''All points'', click on ''Run''
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/10fe5ab0-8df2-47e5-9eba-306956653b30/2008-09-25_1953.png"></div></htm>

*Successful ''Done'' message
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/bd17559d-c349-47be-b0f1-29096dd98a08/2008-09-26_1609.png"></div></htm>

==Admire the result==
You can now proceed to create a model simulation after you [[How to generate tide for Mohid?|create the tidal gauges]]
<htm><div style="width:100%;text-align:center"><img width="70%" src="http://content.screencast.com/users/GRiflet/folders/Jing/media/4d8b4943-0201-4a20-908d-88beb0327c03/2008-09-25_2022.png"></div></htm>

==Next steps==
*[[How_to_generate_tide_for_Mohid%3F|How to generate tide for Mohid?]]

==Previous steps==
*[[Software to run Mohid]]

==About the screen capturing tool==
The screen capturing tool used for this tutorial was the [http://www.jingproject.com/ Jing Project].

[[Category:Graphical User Interfaces]]
[[Category:Help]]
[[Category:Mohid Water]]
[[Category:Exercises]]
[[Category:Example]]
[[Category:How To]]

*NIX platforms

2008-10-22T13:54:05Z

192.168.20.177: /* Building MohidWater */

== Installing ==

=== Prerequisites ===

''NOTE'': this article was written assuming the fortran compiler is ''Intel''. If this is not the case then change where there is written "ifort" with the fortran compiler in use (ex: pgf90, g90, etc...).

==== HDF5 libraries ====
To compile Mohid it is mandatory to have the HDF5 [http://hdf.ncsa.uiuc.edu/HDF5/] libraries compiled. In HDF5's web page it is possible to obtain both binary distribuitions and the source code. Most of the times it is necessary to build from source which takse the following steps:
# download the source code, e. g. hdf5-1.6.5.tar.gz;
# <code> > tar -zxvf hdf5-1.6.5.tar.gz</code>
# <code> > cd hdf5-1.6.5</code>
# <code> > F9X=ifort ./configure --enable-fortran (--prefix=$HDF5ROOTDIR --enable-parallel)</code>
# <code> > make</code>
# <code> > make check</code>
# <code> > make install</code>
Libraries may be found in ./hdf5/lib/ and, typically, in /opt/hdf5/hdf5/lib. Detailed information may be found in file ./release_docs/INSTALL .

==== Zlib libraries ====
To use the HDF5 libraries it is mandatory to have installed the zlib libraries. So install the zlib package for your linux distro. Also, keep a record of where the libz.a library is installed (it might come in handy later on).#

==== Netcdf libraries ====
The netcdf libraries are optional since they are not required to run [[MohidWater]]. However they are useful for other modules of the Mohid Suite such as [[ConvertToHDF5]]. You can get them from the [http://www.unidata.ucar.edu/software/netcdf/ official site]. Here's the [[netcdf|report]] on how to build them for windows.

==== Makefiles ====
Make sure you always have the latest version of the Makefiles from the [[SourceSafe]]. Or,
get a [http://www.mohid.com/hydrogroup/archive.xml test version] of the makefiles from the [http://www.mohid.com/hydrogroup/index.xml hydrogroup page].

==== [[sos|Soscmd]] (optional) ====
The Source-Off site is a program that allows you to obtain the latest version of the code. This is for advanced users only. If you already have a mohid distro with the source code, then don't bother with this.

To obtain the [[sos|soscmd]] client go to [http://www.sourcegear.com/sos/downloads.html this] page.

To obtain the latest Mohid version
#configure the file <code> > makefiles/nix.sos</code>
##Give it the server name usually <code>SERVER=sos.mohid.com</code>
##Type in your sourcesafe username and password in <code>USER</code> and in <code>PASS</code>
##Type in you home directory where the ''.iky'' and ''.key'' files are enclosed. That's it for the configuration!
#--------Users: fill these lines with your sourcesafe data-------------
SERVER :=
USER :=
PASS :=
SOSHOME :=
PROJECT := $(basename $(TARGET))
GET := soscmd -command GetFile \
-server $(SERVER):8890 \
-name $(USER) -password $(PASS) \
-database "W:\SourceSafe\Mohid_v4\srcsafe.ini" \
-project $(PROJECT) \
-soshome $(SOSHOME) \
-file
S := sos
#--------End of sourcesafe data-------------

# type <code> > make nix.sos</code>

=== Building MohidWater ===
To compile MohidWater using the makefiles from the main path, first make sure the source file ending is capitalized (F90, not f90). Afterwards, execute the compilation steps:
# <code> > for i in `find . | grep .f90 | grep -v 'GOTMvar'`; do mv $i `echo $i | sed -e 's/f90/F90/'`;done</code>
# <code> > source /opt/intel/fc/9.0/bin/ifortvars.sh</code>
# <code> > make nix</code>

The first line is required because linux is sensitive to capitalization whereas windows wasn't. The second line is required in order to properly configure intel fortran 9.0 to work. It may be unnecessary in future versions of intel fortran.

To clean the distribution, type:
# <code> > make nix.clean</code>

== Developping [[makefile]]s ==

To develop new makefiles for future or current modules, edit the [[makefile]] in the [[Module Shell]] from the [[Mohid]] [[SourceSafe]]. Please bear in mind that it must work under
in windows, as well as under linux.

=== Using [[sos|SourceOffSite]] in the [[makefile]] ===

An interesting feature of the makefiles would be that they automatically access the [[SourceSafe]]
repository. To do so one can use the [[sos|soscmd]] command line client. An example can be found on the [[*NIX platforms|Sample makefile]].

To use it type:
# <code> > make nix.sos</code>

== TroubleShooting ==

'''Q: the makefile keeps giving me errors :('''

A:Here's a list of what could be causing these errors:
#Open the makefiles and check that fields are properly filled.
#Make sure that '''mod''' and '''bin''' directories exist in the module's folder. Otherwise simply make them with the mkdir command.
#Make sure that "ifort" is a valid command. If it isn't then you probably didn't loaded its environment variables. Type "source /opt/intel/fc/9.0/bin/ifortvars.sh" for that.
#Make sure that the intel fortran compiler was properly installed.

'''Q: the makefile complains when compiling ModuleGOTM.f90'''

A: Probably you have to rename
: GOTM'''V'''ariables_in.'''f90''' ---> GOTM'''v'''ariables_in.'''f90'''
: GOTM'''V'''ariables_out.'''f90''' ---> GOTM'''v'''ariables_out.'''f90'''.
This error shows up in linux because it's case-sensitive whereas windows isn't. Also, make sure that the extension is written in lower case.

'''Q: By the time i'm linking the final MohidWater binary I get some error about
unreferenced functions "compress2" and others in HDF5 files...'''

A: Probably you need to specify to link against the libz.a library. Identify the exactly
the location of libz.a (ex: in my system it can be found at /opt/zlib/lib/libz.a)
then add the following line in MohidWater makefile:

LIBS_NIX = \
$(BASE2LIB) \
$(BASE1LIB) \
$(LIB_HDF5_NIX)/libhdf5_fortran.a \
$(LIB_HDF5_NIX)/libhdf5.a \
$(LIB_HDF5_NIX)/libhdf5_hl.a \
$(LIB_NETCDF_NIX)/libnetcdf.a \
/opt/zlib/lib/libz.a

==See also==
*[[Makefile]]
*[[Mohid Makefile]]

[[Category:Technology]]
[[Category:Linux]]
[[Category:Makefile]]

Thredds

2008-10-22T12:25:16Z

192.168.20.177:

[[Thredds]] (Thematic Realtime Environmental Distributed Data Services) is a tomcat servlet that serves xml catalogs of [[openDAP]] datasets.

==Setup==
A working [[tomcat]] server is a prerequisite. Simply '''copy the thredds.war file''' obtained from the thredds homepage '''into the''' [[tomcat]] '''webapps directory'''.

===data.mohid.com===
*'''How do I restart the [[tomcat]] and thredds server in data.mohid.com?'''
> cd /home/guillaume/Software/las7/tomcat/tomcat/bin
> ./Tomcat5.sh start

*'''How do I know if tomcat is running?''':
> netstat -tlnap | grep 8080

==Directory tree structure==

===$TOMCAT_HOME/content/thredds===
*'''catalog.xml''': catalog file containing all the netcdf datasets.

==Building thredds urls==
===Dataset===
* Viewing a ${catalog} file tree named ${catalog}.xml:
http://data.mohid.com:8080/thredds/${catalog}.html

* Viewing a specific ${dataset} thredds metadata:
http://data.mohid.com:8080/thredds/${catalog}.html?dataset=${dataset.id}

* Viewing a specific ${dataset}:
http://data.mohid.com:8080/${dataset.service.base}/${dataset.urlpath}

===DatasetScan===
* Viewing a particular ${datasetscan} tree from any ${catalog} in the thredds server:
http://data.mohid.com:8080/thredds/catalog/${datasetscan.path}/catalog.html

* Viewing a specific ${datasetscan.filteredfilename} thredds metadata:
http://data.mohid.com:8080/thredds/catalog/${datasetscan.path}/catalog.html?dataset=${datasetscan.id}/${datasetscan.filteredfilename}.nc.html

* Viewing a specific ${datasetscan.filteredfilename} dataset:
http://data.mohid.com:8080/${datasetscan.service.base}/${datasetscan.path}/${datasetscan.filteredfilename}.nc.html

==A sample catalog file==
<code>[XML]

<?xml version="1.0" encoding="UTF-8"?>

<catalog name="MOHID THREDDS Server Catalog"
xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0"
xmlns:xlink="http://www.w3.org/1999/xlink">

<service name="MOHID DODS" serviceType="OpenDAP" base="/thredds/dodsC/" />
<datasetRoot path="test" location="content/testdata/"/>

<dataset name="Test Single Dataset" ID="testDataset" serviceName="MOHID DODS"
urlPath="test/testData.nc"/>

<datasetScan name="Test all files in a directory" ID="testDatasetScan"
path="testAll" location="content/testdata">

<metadata inherited="true">
<serviceName>MOHID DODS</serviceName>
</metadata>

<filter>
<include wildcard="*.nc"/>
</filter>

</datasetScan>

<catalogRef xlink:title="Test Enhanced Catalog" xlink:href="enhancedCatalog.xml" name=""/>

</catalog>
</code>

==See also==
*[[Tomcat]]
*[[OpenDAP]]
*[[LAS]]

==External references==
*[http://www.unidata.ucar.edu/projects/THREDDS/tech/tutorial/GettingStarted.html Getting started]
*[http://data.mohid.com:8080/thredds/catalog.html MOHID Thredds data server]

[[Category:Linux]]

Tomcat

2008-10-22T12:18:02Z

192.168.20.177: /* Faqs */

The apache tomcat is a jsp (java servlet pages) server. It's similar to an http server like the apache server, only it serves jsp. It is required in order to use [[Thredds]] or [[LAS]].

==Setting up==
> cd /home/guillaume/Software/las7
> mkdir tomcat
> cd tomcat
> wget http://neacm.fe.up.pt/pub/apache/tomcat/tomcat-5/v5.5.26/bin/apache-tomcat-5.5.26.tar.gz
> tar -xzf apache-tomcat-5.5.25.tar.gz
> ln -s apache-tomcat-5.5.25/ tomcat

Edit the <code>apache-tomcat-5.5.25/conf/server.xml</code> and change the ports (default:8080) if needed.

To run the tomcat as a daemon service, one needs to compile the <code>jsvc</code> program:
> cd ./tomcat/bin
> tar xvfz jsvc.tar.gz
> cd jsvc-src
> ./configure --with-java=/usr/java
> make
> cp jsvc ..
> cd ..

==The tomcat files tree==
===/bin===
* '''./jsvc''' : the loader that runs tomcat as a daemon ( > jsvc -help)
* '''[[tomcat bash|./Tomcat5.sh start|stop]]''': the custom bash script that starts or stops the tomcat server

===/conf===
* '''server.xml''': where one defines which ports for tomcat to use.
* '''tomcat-users.xml''': where one defines who are the valid users for the tomcat server and what are their roles (privileges)

===/log===
* '''catalina.out''': where one can check the logs and errors issued by the boot and running of the tomcat server.

===/webapps===
Webapps the root directory where all the .war files (the tomcat servlets) go. Ex: [[thredds]].

==Faqs==
*'''How do I restart the tomcat and thredds server in data.mohid.com?'''
> cd /home/guillaume/Software/las7/tomcat/tomcat/bin
> ./Tomcat5.sh start

*'''How do I know if tomcat is running?''':
> netstat -tlnap | grep 8080

==External references==
*[http://tomcat.apache.org/tomcat-5.5-doc/introduction.html tomcat homepage]

[[Category:Linux]]

Fecal coliforms

2008-10-17T10:19:05Z

192.168.20.177:

A lot can be said about fecal coliforms. Basically they're a pollutant that is found in sewer discharges in large quantities.

==Stats==

*typical concentrations at a local discharge: '''1e7 to 1e8 coli/100 mL'''
*typical discharge flow: '''1 m3/s per 250,000''' inhabitants. Guia de Cascais is 2 m3/s.
*typical decay time (decimation):
**Summer sunny day: 30 min
**Night: 24h
**'''Average: 2 h'''
*Clean bathing water treshold issued by the European Bathing Water Directive: '''100 coli/100 mL'''

Fecal coliformes

2008-10-17T10:18:58Z

192.168.20.177:

#REDIRECT [[Fecal coliforms]]

Google Earth

2008-10-10T15:05:16Z

192.168.20.177:

[[Google Earth]] is the openGL GIS client program that maps all the worlds orthophotomaps. It's an important tool to extract coastlines and other baseline georeferenced data in [[kml]] format.

==Configure Google Earth==
*From the ''tools'' menu, select ''options''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/1406fee0-feba-4a4d-812f-16a3585219c4/2.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/1406fee0-feba-4a4d-812f-16a3585219c4/2.png" width="404" height="218" border="0" /></a></htm>

*Select ''decimal degrees'', then ''apply'' and click ''ok''
<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/d1b89d8b-de12-4f48-9ea5-58c888dae3cf/2008-10-10_1611.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/d1b89d8b-de12-4f48-9ea5-58c888dae3cf/2008-10-10_1611.png" width="737" height="519" border="0" /></a></htm>

==External links==
*[http://earth.google.com Google Earth]

[[Category:Google]]

ConvertToXYZ

2008-10-07T13:03:38Z

192.168.20.177: /* SRTM30 */

[[ConvertToXYZ]] is a small tool that extracts baseline three-dimensional data into [[XYZ points |XYZ points files]]. It is useful, for instance, to extract baseline data to create bathymetries.

== Quick Start ==
#Map a network drive to the data file (ETOPO, GEBCO, NOAA etc...).
#Create and edit a ''ConvertToXYZ.dat'' file. Save it in the same path of the executable.
#Run the executable.

== Options file ==

'' '''WARNING:''' Only use integer coordinate lat/lon numbers''.

===ETOPO2'===

Here's what the options ''ConvertToXYZ.dat'' file looks like:
<begin_window>
FILE_TYPE : 2
INPUT_FILENAME : Z:\etopo2.dat
OUTPUT_FILENAME : WestIberiaET2.xyz
TOP : 46
BOTTOM : 33
LEFT : -14
RIGHT : -5
MAXIMUM : 1
MINIMUM : -9999
WRITE_AS_BATHYMETRY : 1
CONVERT_TO_HDF5 : 0
<end_window>

===SRTM30===
''Caution: make sure the ORIGIN_X and ORIGIN_Y correspond to the origin of the srtm30 original source file!''

<begin_window>
FILE_TYPE : 7
TOP : 46
BOTTOM : 33
LEFT : -14
RIGHT : -5
MAXIMUM : 1
MINIMUM : -9999
INPUT_FILE : \\kepler\DataCenter1\DataCenter\DadosBase\Oceanografia\Batimetria\SRTM30\Data\w020n40.Bathmetry.srtm
XYZ_OUTPUT_FILENAME : WestIberiaSRTM.xyz
ORIGIN_X : -20
ORIGIN_Y : 40
<end_window>

==See also==
*[[Digital_Terrain_Creator|Digital Terrain Creator]]

[[Category:Tools]]

Module Discharges

2008-10-07T10:09:13Z

192.168.20.177:

== Overview ==
Module Discharges handles all the point discharges in Mohid Water Modelling System. These discharges can be simple water discharges but can also have properties such as substances concentration (temperature, salinity, nutrients, contaminants, etc) and/or momentum.

== Main features ==

=== ID ===

=== Location ===

=== Database file ===

=== Properties ===

== User manual ==

===Sample discharge===
Here's what a configuration file of the [[Module Discharges]] should look like for a single river run-off. Note that you are previously required to build a time serie .srw with the flow, the temperature and the salinity in order to correctly implement the discharge.

<begindischarge>
NAME : Loire
DESCRIPTION : Daily timeserie for the year 2004
I_CELL : 144
J_CELL : 220
DEPTHBYGRID : 1
K_CELL : 38
DEFAULT_FLOW_VALUE : 300
DATA_BASE_FILE : M:\Biscay\GeneralData\Level2\rivers\Loire.srw
FLOW_COLUMN : 2
TIME_SERIE_COLUMN : 1
DISCHARGE_UNIFORM : 1

<<beginproperty>>
NAME : temperature
UNITS : celcius
DESCRIPTION : temperature in the tagus river
CONSTANT_CONC : 0
DEFAULTVALUE : 19.9
TIME_SERIE_COLUMN : 3
<<endproperty>>

<<beginproperty>>
NAME : salinity
UNITS : psu
DESCRIPTION : salinity in the tagus river
CONSTANT_CONC : 1
DEFAULTVALUE : 0.01
<<endproperty>>

<enddischarge>

== References ==

[[Category:Modules]]
[[Category:MOHID Base 1]]

Ajudas de custo

2008-10-06T16:09:04Z

192.168.20.177:

==2008==
*Extracto do regulamento de despesas do IST

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/3b6d8cdb-dff4-4aa6-bda2-90d336f7698d/2008-10-06_1716.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/3b6d8cdb-dff4-4aa6-bda2-90d336f7698d/2008-10-06_1716.png" width="727" height="286" border="0" /></a></htm>

*Extracto da folha de excel da Filipa

<htm><a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/bf9f100d-b37a-47a2-b528-54c214d561e9/2008-10-06_1717.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/bf9f100d-b37a-47a2-b528-54c214d561e9/2008-10-06_1717.png" width="656" height="384" border="0" /></a></htm>

How to generate tide for Mohid?

2008-10-03T09:05:32Z

192.168.20.177: /* That's it! */

Once you [[How_to_create_a_model_gridded_bathymetry%3F|created a gridded bathymetry]], before you run the model simulation, you may want to generate the tidal gauges that will generate the tide at the open-boundaries during the simulation.

==Step 1 - Create the tidal gauges points in the GIS==

===Create a new points layer in GIS===
*Make sure that you already have created your bathymetric gridded data file and that it's currently open in your GIS project. Now, simply add a new data item from the menu:
<htm>
<img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/eb1787b2-17a3-44e8-9afd-6ebffd39b685/2008-09-30_1338.png" ></img>
</htm>

*Select ''XYZ'' type, then click on ''Browse''
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/c9537831-a605-445f-a0a9-0bdc06906b83/2008-09-30_1458.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/c9537831-a605-445f-a0a9-0bdc06906b83/2008-09-30_1458.png" width="408" height="201" border="0" /></a>
</htm>

*Choose a name for the tidal gauge points, then hit save:
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/be0f8565-672b-4cba-a0eb-2d4e0740f380/2008-09-30_1501.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/be0f8565-672b-4cba-a0eb-2d4e0740f380/2008-09-30_1501.png" width="563" height="412" border="0" /></a>
</htm>

*Hit the Ok button
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/b8297648-3a07-4420-b8e3-b116ba98b09b/2008-09-30_1503.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/b8297648-3a07-4420-b8e3-b116ba98b09b/2008-09-30_1503.png" width="408" height="201" border="0" /></a>
</htm>

===Edit the points layer===

*Type ''4'' in the size text-box, and then select settings:
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/bf8b6f9c-bcc7-466d-9d35-754f02dfffad/2008-09-30_1514.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/bf8b6f9c-bcc7-466d-9d35-754f02dfffad/2008-09-30_1514.png" width="744" height="457" border="0" /></a>
</htm>

*Select option ''Constant'', then click on Pick Color (a new window pops up), then select a bright color and hit Ok on the new window (it will make the new window close), then click on Ok, and the new configuration will be enabled.
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/9af53612-cdcc-42a2-8446-754cfdf804d8/2008-09-30_1520.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/9af53612-cdcc-42a2-8446-754cfdf804d8/2008-09-30_1520.png" width="557" height="349" border="0" /></a>
</htm>

*Close and comply with changes by hitting the Ok button
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/163854df-1db9-432a-b279-e1867a45ce25/2008-09-30_1530.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/163854df-1db9-432a-b279-e1867a45ce25/2008-09-30_1530.png" width="463" height="153" border="0" /></a>
</htm>

===Add the tidal gauges to the points layer===

*Select the ''TideGaugesTest.xyz'' points layer, then select the add a point command:
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/3134eee5-3701-4f8f-9bb0-a47c93c96694/2008-09-30_1535.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/3134eee5-3701-4f8f-9bb0-a47c93c96694/2008-09-30_1535.png" width="641" height="224" border="0" /></a>
</htm>

*Hit Ok ...
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/c0d2df5d-4eb1-4e46-b868-acc7018ffea6/2008-09-30_1543.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/c0d2df5d-4eb1-4e46-b868-acc7018ffea6/2008-09-30_1543.png" width="300" height="129" border="0" /></a>
</htm>

*Click to add points all along the open boundaries, roughly 10 cells wide apart:
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/36056d54-9fe7-4c84-88db-7aead37b98e1/2008-09-30_1548.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/36056d54-9fe7-4c84-88db-7aead37b98e1/2008-09-30_1548.png" width="467" height="304" border="0" /></a>
</htm>

*Keep adding those points alternatively on each side of the open-boundary
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/2eeb79f5-2b64-4939-af45-15a71a3218af/2008-09-30_1552.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/2eeb79f5-2b64-4939-af45-15a71a3218af/2008-09-30_1552.png" width="806" height="471" border="0" /></a>
</htm>

*Final look:
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/208fa9ed-3cd2-4d8a-bc1b-439f38a7c3a9/2008-09-30_1555.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/208fa9ed-3cd2-4d8a-bc1b-439f38a7c3a9/2008-09-30_1555.png" width="550" height="532" border="0" /></a>
</htm>

===Save the tidal gauges points layer===

*From the ''Data Items'' menu, select the ''Save All'' option
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/59c74f4a-e0b3-4972-8373-aa2a17f45c63/2008-09-30_1558.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/59c74f4a-e0b3-4972-8373-aa2a17f45c63/2008-09-30_1558.png" width="610" height="293" border="0" /></a>
</htm>

==Step 2 - Generate the tidal gauges from FES2004==

In order to generate tidal gauges from FES2004, you will need to obtain the data file and the program that performs the extraction into MOHID tidal-gauge format. [[Fes2004|Here]] you will find details about that.

*Get the [http://maretec.mohid.com/PublicData/products/Software/Mohid-Tide_v0.4.zip mohid-tide] package and extract it somewhere on your disk;
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/d0f50330-735c-4f46-98c2-ac0b2d2837fc/2008-09-30_1759.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/d0f50330-735c-4f46-98c2-ac0b2d2837fc/2008-09-30_1759.png" width="455" height="237" border="0" /></a>
</htm>

*Transfer the xyz file to the mohid-tide folder. ''WARNING: Remove any blank lines from the xyz file!''
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/f46bb001-c0a6-4550-856c-f289c69444f8/2008-09-30_1818.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/f46bb001-c0a6-4550-856c-f289c69444f8/2008-09-30_1818.png" width="432" height="455" border="0" /></a>
</htm>

*Edit the run-tide.bat accordingly to the following example:
>mohid-tide ..\fes2004data\tide.nc TideGaugesTest.xyz output.dat 0 2.08
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/02c18beb-569b-4a07-82a9-52a7bc824b41/2008-09-30_1810.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/02c18beb-569b-4a07-82a9-52a7bc824b41/2008-09-30_1810.png" width="939" height="404" border="0" /></a>
</htm>

*Run the batch file. This will create the tidal gauge file.
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/fd5be2bd-445a-4baf-a412-10111385c3d2/2008-09-30_1831.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/fd5be2bd-445a-4baf-a412-10111385c3d2/2008-09-30_1831.png" width="674" height="417" border="0" /></a>
</htm>

*Verify if your tidal gauge file is correctly formed. Edit it and inspect.
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/639f1a32-a94a-4107-b287-863ae152a039/2008-09-30_1838.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/639f1a32-a94a-4107-b287-863ae152a039/2008-09-30_1838.png" width="673" height="556" border="0" /></a>
</htm>

===That's it!===
If all went well, then you have a valid gridded bathymetry for the domain and you have tidal gauges extracted from the [[Fes2004]] solution that will generate tide to the model. You're ok to start building a project using [[Mohid GUI]].

==Next steps==
*Read the [[Mohid GUI]] to create a new simulation project then,
*[[How to configure a 2D model forced with tide with MOHID]]

==About the screen capturing tool==
The screen capturing tool used for this tutorial was the [http://www.jingproject.com/ Jing Project].

[[Category:Graphical User Interfaces]]
[[Category:Help]]
[[Category:Mohid Water]]
[[Category:Exercises]]
[[Category:Example]]
[[Category:Tools]]
[[Category:How To]]

How to create a bathymetry

2008-09-26T11:40:52Z

192.168.20.177:

#Redirect [[How_to_create_a_model_gridded_bathymetry%3F]]

Tide Preview

2008-09-24T13:58:08Z

192.168.20.177: /* See also */

[[Tide Preview]] allows to generate a tide timeserie from the harmonic consituents of a given tidal gauge.

Configuration of the '''TidePrevInput.dat''' file:

START : YYYY MM DD HH MM SS - !Start time to compute water level
END : YYYY MM DD HH MM SS - !End time to compute water level
DT : real - !Time step to compute water level
EXPORT_TO_XYZ : 0/1 0 !Create a XYZ file with gauge locations
XYZ_FILE : char - !Name of XYZ file to be created

<begintideprev>
IN_TIDES : char - !Path to gauge file
OUT_FILE : char - !Path to output water level time serie file
<endtideprev>

Sample IN_TIDES file:

<begingauge>
NAME : nth test
LONGITUDE : -16.0000 33.0000 15.0000
LATITUDE : 15.0000 44.0000 35.0000
METRIC_X : -16.5543
METRIC_Y : 15.7432
REF_LEVEL : 2.08000
TIME_REF : 0.000000
M2 : 0.432953 -88.0402
S2 : 0.166823 -51.6513
K1 : 0.0566607 -4.53947
K2 : 0.0460439 -54.6424
N2 : 0.0820980 -108.615
2N2 : 0.0104858 -129.940
O1 : 0.0396148 -104.233
Q1 : 0.0186481 -4.40105
P1 : 0.0121636 -161.633
M4 : 0.000000 0.000000
Mf : 0.0140184 -1.40625
Mm : 0.00688141 -4.94457
Mtm : 0.00290994 2.06745
MSqm : 0.000401051 4.38925
<endgauge>

[[Category:Tools]]

Tideprev

2008-09-24T13:20:58Z

192.168.20.177:

#REDIRECT [[Tide Preview]]

Mohid Support Tools

2008-09-23T14:09:19Z

192.168.20.177: /* Pre-processing */

== Overview ==

MOHID Water Modelling System has a large variety of support tools used to help creating simulations, preparing and processing input and output data files. Below is a list of the support tools built around MOHID.

== Pre-processing ==
*[[AssimilationPreProcessor]]
*[[AssimilationZones]]
*[[BasinDelimiter]]
*[[Box2GridData]]
*[[ConvertToHDF5]]
*[[ConvertToXYZ]]
*[[CopyMohidProject]]
*[[Digital Terrain Creator]]
*[[FillMatrix]]
*[[Fes95]]
*[[Fes2004]]
*[[FilterBathymetry]]
*[[GenerateGrid]]
*[[HydrodynamicAnalyser]]
*[[InvertedBarometer]]
*[[Kml2Mohid]]
*[[NOAAnetcdfTOhdf5]]
*[[SmoothBatimNesting]]
*[[Tide Preview]]
*[[TimeSeriesCreator]]

== Post-processing ==
*[[ConvertToTimeSerie]]
*[[MovingTimeSerie]]
*[[MovingProfile]]
*[[TidalGaugeCharts]]
*[[Convert2netcdf]]

== HDF5 tools ==
*[[HDF5Extractor]]
*[[HDF5Exporter]]
*[[HDF5Operator]]
*[[HDF5Statistics]]

== [[MatLab]] Tools ==
*[[MatLab_Tools|Various tools]]: includes reading and plotting MOHID HDF5.
*[[MatLab_Timeseries|Timeseries]]
*[[MatLab_TideAnalyser|TideAnalyser]]

== Time Series tools ==
*[[Mohid Statistics Analyser]]
*[[JoinTimeSeries]]

== Others ==
*[[CoordTrans]]
*[[MohidReservoirOptimization]]
*[[SWAT Link]]

== Not developed by the MOHID team ==
*[[Sos|Source OffSite]]
*[[SourceSafe]]
*[[OpenDAP]]
*[[LAS]]
*[[Wiki]]
*[[H5DUMP]]
*[[SeaDAS]]
*[[Notepadplus]]

[[Category:Tools]]
[[Category:Hdf5]]

Kml2Mohid

2008-09-23T10:58:05Z

192.168.20.177: /* Other platforms */

[[Kml2Mohid]] is a little program that converts [[Google Earth]] [[kml]] files into Mohid [[GIS]] data files. It's quite useful to quickly create coastlines in [[Google Earth]].

==Syntax==
Open a command-line window and type:

> [http://www.mohid.com/hydrogroup/data_sources/kml2mohid.exe kml2mohid.exe] MyGEDataFile.kml

It may output a point file (.xyz), a line file (.lin) and/or a polygon file (.xy) depending if it finds relevant data in the [[kml]] file.

==Other platforms==
Alternatively, you may install [[ruby]] and use the ruby [http://www.mohid.com/hydrogroup/data_sources/kml2mohid.rb source code] (~80 lines). Eventually one may create a local executable with the [[ruby#Features|rubyscript2exe]] module.

> ruby [http://www.mohid.com/hydrogroup/data_sources/kml2mohid.rb kml2mohid.rb] MyGEDataFile.kml

[[Category:Programming]]
[[Category:Tools]]

Kml

2008-09-22T20:28:32Z

192.168.20.177:

[[KML]] is the Keyhole Markup Language. It's an [[xml]]-based language that allows to create content for Google Earth and Google Maps.

It allows to create [[viewpoints]], [[placemarks]], [[paths]], [[shapes]], [[image overlays]] and [[3D buildings]]. It also allows to embed customized [[html]] code in the [[placemarks]].

==Sample kml file==

=== Placemarks with custom html code ===
[http://maps.google.com/maps?f=q&q=http%3A%2F%2Fnfist.ist.utl.pt%2F%7Eguillaume%2FMohidBeachcams_NetL.kml&btnG=Search+Maps Here's] a simple [[kml]] file that adds a [[placemark]], a [[viewpoint]] for it, and embeds some custom html code:

<?xml version="1.0" encoding="UTF-8"?>
<kml xmlns="http://earth.google.com/kml/2.2">

<Document>

<name>MohidBeachCams.kml</name>

<visibility>1</visibility>

<Folder>

<name>Portugal Beach Cams</name>

<visibility>1</visibility>

<description>
<![CDATA[
Live data from <a href="http://cams.beachcam.pt/">Beachcam_PT</a>
and <a href="http://www.surftotal.com/webcams2/Default.htm">SurfTotal webcams</a>.
Best viewed when using GE built-in web browser.
Tools -> Options -> Preferences -> Navigation bar -> Uncheck "Show web results in external browser".
]]>
</description>

<LookAt>
<longitude>-9.285977261935919</longitude>
<latitude>38.7380813109443</latitude>
<range>47801.2002729008</range>
<tilt>2.43637162447063e-011</tilt>
<heading>0.01425072853298695</heading>
</LookAt>

<Placemark>

<name>Praia do Guincho</name>

<LookAt>
<longitude>-9.470984593789977</longitude>
<latitude>38.73175408910536</latitude>
<range>1421.36386586457</range>
<tilt>2.897405864852683e-010</tilt>
<heading>-0.08870325629105799</heading>
</LookAt>

<styleUrl>#camneutra</styleUrl>

<Point>
<coordinates>-9.472970249051258,38.73236056451183,0</coordinates>
</Point>

<description>
<![CDATA[
Looking from Praia do Guincho.
<img src="<code>http://cams.beachcam.pt//camaxis/guincho_00001.jpg</code>">
Surf report <a href="http://cams.beachcam.pt/praias_beachcams.php?id=18">here</a>.
Live cam <a href="http://www.surftotal.com/webcams2/guincho_cam.asp?id=25">here</a>.
]]>
</description>

</Placemark>

</Folder>

</Document>

</kml>

=== Network links ===
[[Network links]] can be very useful when providing early releases of beta services. This way, the developper may continue to upgrade the production version of the [[kml]] file, by providing to the users a file that contains a link to it.

[http://maps.google.com/maps?f=q&q=http%3A%2F%2Fnfist.ist.utl.pt%2F%7Eguillaume%2FMohidBeachcams_NetL.kml&btnG=Search+Maps Here's] a simple kml file that adds a [[network link]] to another [[kml]] file:

<?xml version="1.0" encoding="UTF-8"?>
<kml xmlns="http://earth.google.com/kml/2.2">
<NetworkLink>
<name>MohidBeachcams</name>
<open>1</open>
<flyToView>1</flyToView>
<Url>
<href>http://nfist.ist.utl.pt/~guillaume/BeachCams_PT.kml</href>
<refreshMode>onInterval</refreshMode>
<refreshInterval>50</refreshInterval>
<viewRefreshMode>onRegion</viewRefreshMode>
</Url>
</NetworkLink>
</kml>

=== Image overlays ===

=== Regions ===

=== Time ===

==Kml2Mohid==

[[Kml2Mohid]] is a little [[ruby]] program that converts [[Google Earth]] [[kml]] files into Mohid [[GIS]] data files.

==External References==
*[http://code.google.com/apis/kml/documentation/index.html Kml reference documentation]
*[http://maps.google.com/maps?f=q&q=http%3A%2F%2Fnfist.ist.utl.pt%2F%7Eguillaume%2FMohidBeachcams_NetL.kml&btnG=Search+Maps MohidBeachCams]
*[http://earth.google.com Google Earth]
*[http://maps.google.com Google Maps]
*[http://maps.google.com/maps/mm?mapprev=1 Google Mapplets]

[[Category:Technology]]
[[Category:Windows]]
[[Category:Linux]]
[[Category:Google]]

Convert2netcdf

2008-09-11T11:19:19Z

192.168.20.177: /* Example */

== Overview ==
'''Convert2netcdf''' is a tool to convert MOHID results files written in [[HDF5]] format into [[netcdf]].
This tool makes use of [[ModuleNETCDF]] (under development and to be included in [[MOHID Base 1]]). Optionally, you can extract only specified datasets.

== Input data file ==
The input data file must be placed in the working folder and must be named ''Convert2netcdf.dat''.

HDF_FILE : [char] !Path to the HDF5 file to be converted
HDF_SIZE_GROUP : [char] !HDF group containing the HDF dataset from where
!the dimensions will be read
HDF_SIZE_DATASET : [char] !Name of the HDF dataset from where the dimensions
!will be read
HDF_TIME_VAR : [char] !Name of the HDF group containing the
!time values
HDF_READ_LATLON : int !Type of projection (0 - metric, 1 - lat/lon)
HDF_READ_SIGMA : int !Type of vertical coordinate (0 - cartesian, 1 - sigma)

IMPOSE_MASK : bool !In case we want to specify the mask variable.
HDF_MASK : [char] !If we chose to specify a mask variable, then we define here
!the variable name
HDF_MASK_IS_3D : bool !Is the mask variable 3D? yes or no.
RESULTS_ARE_2D : bool !Sometimes the mask variable is 3D, but the results

CONVERT_EVERYTHING : int !0 - Don't convert everything, 1 - Convert everything
VGROUP_TO_CONVERT : [char] !Path to dataset(s) to converto. (e.g. /Results/water level)

NETCDF_FILE : [char] !netcdf file to be created
NETCDF_TITLE : [char] !netcdf file title
NETCDF_CONVENTION : [char] !netcdf naming convention
NETCDF_VERSION : [char] !netcdf library version
NETCDF_HISTORY : [char] !netcdf file history
NETCDF_SOURCE : [char] !netcdf file source
NETCDF_INSTITUTION : [char] !netcdf institution
NETCDF_REFERENCES : [char] !netcdf references
NETCDF_DATE : int !current year

== Example ==

HDF_FILE : WaterProperties_1.hdf5
HDF_SIZE_GROUP : /Grid
HDF_SIZE_DATASET : WaterPoints3D
HDF_TIME_VAR : Time
HDF_READ_LATLON : 1
CONVERT_EVERYTHING : 0
VGROUP_TO_CONVERT : /Results/salinity

NETCDF_FILE : WaterProperties_1.nc
NETCDF_TITLE : WaterProperties file converted to netcdf
NETCDF_CONVENTION : CF-1.0
NETCDF_VERSION : 3.6.1
NETCDF_HISTORY : Converted from hdf5
NETCDF_SOURCE : File created by MOHID-Convert2ncdf
NETCDF_INSTITUTION : Instituto Superior Técnico (IST)
NETCDF_REFERENCES : http://www.mohid.com/
NETCDF_DATE : 2006

[[Category:Tools]]

Google ajax api

2008-09-08T14:25:33Z

192.168.20.177:

Here's a sample usage of the [[Google ajax api]]. This api is best combined with [[jQuery]].

jQuery.get(http://ajax.googleapis.com/ajax/services/search/web?v=1.0&q=cocu&btnI=kudos)
=>
{ "responseData": {
"results":[{
"GsearchResultClass":"GwebSearch",
"unescapedUrl":"http://en.wikipedia.org/wiki/Phillip_Cocu",
"url":"http://en.wikipedia.org/wiki/Phillip_Cocu",
"visibleUrl":"en.wikipedia.org",
"cacheUrl":"http://www.google.com/search?q\u003dcache:ffIT9MMI2OgJ:en.wikipedia.org",
"title":"Phillip \u003cb\u003eCocu\u003c/b\u003e - Wikipedia, the free encyclopedia",
"titleNoFormatting":"Phillip Cocu - Wikipedia, the free encyclopedia",
"content":"Phillip John William \u003cb\u003eCocu\u003c/b\u003e (born October 29, 1970 in Eindhoven, Noord-Brabant) is a former Dutch football midfielder who is currently an assistant manager of \u003cb\u003e...\u003c/b\u003e"
}, {
"GsearchResultClass":"GwebSearch",
"unescapedUrl":"http://french.about.com/library/weekly/aa020901t.htm",
"url":"http://french.about.com/library/weekly/aa020901t.htm",
"visibleUrl":"french.about.com",
"cacheUrl":"http://www.google.com/search?q\u003dcache:doki3cm1bD4J:french.about.com",
"title":"\u003cb\u003eCocu\u003c/b\u003e - Gestes français - French Gestures",
"titleNoFormatting":"Cocu - Gestes français - French Gestures",
"content":"\u003cb\u003eCocu\u003c/b\u003e literally means \u0026quot;cuckold.\u0026quot; Hold your index fingers up next to your ears and wiggle them up and down. Register - vulgar \u003cb \u003e...\u003c/b\u003e"

[[Category:Google]]
[[Category:Programming]]

Google

2008-09-08T14:24:02Z

192.168.20.177:

[[Search|Searching google]] can be an art. You can search this [[wiki]] too.

<csegoogle>007941234899421137885:xtadckhl66k</csegoogle>

==Finding certain file types==
filetype:mp3
filetype:pdf
filetype:xspf
filetype:m3u

==[[Google ajax api|Ajax api]]==
How to use the [[Google ajax api]].

==External References==
*[http://www.google.com/ Google]

[[Category:Web]]

Mod-python

2008-09-05T17:01:16Z

192.168.20.177: /* Example */

[[Mod-python]] is a module for the apache web server that allows to run [[python]] scripts and publish html.

==Configuring==

Edit ''/etc/httpd/conf.d/python.conf'' or the ''/etc/httpd/conf/httpd.conf''

LoadModule python_module modules/mod_python.so

<Directory /var/www/html/python>
AddHandler mod_python .py
PythonHandler mod_python.publisher
PythonDebug On
</Directory>

You can also add the following lines in the ''.htaccess'' file from the local user's ''public_html'' directory:
AddHandler mod_python .py
PythonHandler mod_python.publisher
PythonDebug On

==Testing==

/var/www/html/test.html

<html>
<head>
<title>A simple "get month" script</title>
</head>
<body>
<form method="POST" '''action="python/getMonth.py/getMonth"'''>
Show which month for 2005
<select name="month">
<option value="1">January</option>
<option value="2">February</option>
<option value="3">March</option>
<option value="4">April</option>
<option value="5">May</option>
<option value="6">June</option>
<option value="7">July</option>
<option value="8">August</option>
<option value="9">September</option>
<option value="10">October</option>
<option value="11">November</option>
<option value="12">December</option>
</select>
<input type="submit" value="Show Month">
</form>
</body>
</html>

/var/www/html/python/getMonth.py

#!/usr/bin/env python
# A simple script to output a calendar month based off input
# from a web form.
#
import calendar
from mod_python import apache
def getMonth(req,month):
req.write(calendar.month(2005, int(month),2,3))

==Example==

""" Publisher example """
def say(req, what="NOTHING"):
return "I am saying %s" % what

Usage: http://host.com/hello.py/say?what=hi

[[Category:Programming]]
[[Category:Internet]]
[[Category:Python]]

Python

2008-09-05T16:30:32Z

192.168.20.177:

[[Python]] is a rather popular interpreted language allowing object-oriented programming. Built under a modular open philosophy similar to [[Perl|Perl's]], it has a distinct opposite-minded philosophy to the ''There's more than one way to do it'' [[Perl]] moto, which is rather like ''There's one - and no more - obvious way to do it''. This produces uncluttered, clean and readable code.

==Installing modules==
Here's a sample command line for fetching and installing a python module under a bash shell:
> cd ''mymodules''
> wget http://''addressofmodule''/''module''.tar.gz
> tar -xvf ''module''.tar.gz
> cd ''module''
> python setup.py build
> sudo python setup.py install

Should you not be able to "sudo", then you need to install the module in your personal python module path (remember to define the <code>$PYTHONPATH</code> environment variable)
> python setup.py install --home ~/python/imports

===[[Mod-python]]===
[[Mod-Python]] is a module for the apache web server that allows to run python scripts and publish html.

===Numpy and scipy===
====Windows====
Check out this [http://www.scipy.org/Installing_SciPy/Windows link for windows].
====Linux====
=====FC5=====
For Fedora Core 5 (which makes NumPy 0.9.5 and NumPy 0.9.6 available via the fedora-extras yum repository):
yum install numpy
yum install lapack-devel blas-devel
Then download and unzip scipy-0.4.8 to, for example, /usr/local/src/. This version of SciPy is compatible with NumPy 0.9.5 and NumPy 0.9.6.
cd /usr/local/src/scipy-0.4.8
python setup.py install >& install.log

The install log will contain some errors about not finding atlas libraries, and recommending that you set the ATLAS environment variable. But doing this doesn't seem to make any difference, even if the atlas package is installed.

=====FC6=====
Numpy 1.0.1 and SciPy 0.5.2 are available in the fedora-extras yum repository. Installing the SciPy package should automatically cause the various dependencies (including NumPy) to be installed:
yum install scipy

====Test====
Once the binary are installed, test them with
>>> import numpy, scipy
>>> numpy.test()
>>> scipy.test()

===Not a root user?===
Should you not be granted root to the machine and still need to install a python module then add in your .bash_profile file the following code

> vim ~/.bash_profile
.bash_profile> PYTHONPATH=$PYTHONPATH:~/python/imports/lib/python
.bash_profile> export PYTHONPATH

==Best Practices==
Here we shortly define good practices and conventions that are advised to be followed when developping in Python. These will allow easy scalability of Python's code.

===Coding Conventions===
We'll try to keep them simple, short and concise.
When defining '''classes''':
* Name them with a '''capital letter''',
When defining '''data attributes''':
* Use a '''noun''',
When defining '''method attributes''':
* Use a '''verb'''.

===Documenting and commenting===
It's highly advisable to make use of Python's '''pydoc''' command that auto-generates man pages for Python's scripts and modules. Documentation must be inserted between '''"""''' tags.

> pydoc pymodule

===[http://en.wikipedia.org/wiki/Unit_test Unit testing]===
Following the latest hype at Google stating that ''Debugging sucks :( Testing rocks :)'', it's advisable to make use of python's built-in unit testing engine, '''doctest'''.
simply copy and paste python command-line's inputs with the expected outputs inside the documentation tags ('''"""''').

> python pymodule.py -v

===Exploring new modules===
It is recommended to use iPython to easily and quickly inspect new modules in Python. It comes natively with standard major *nix distros. Basically one can then use tabbing for autocompletion in a python command-line environment.
> ipython

===Python best-practice template===

====[http://refactormycode.com/codes/51-classtemplate The script]====
Here's a template python script ('''classtemplate.py''') that makes use of all of the above described coding conventions,
<code>[python,Y]
#! /usr/bin/python
""" A python primer. pydoc, doctest and classes.

Syntax:
To generate man pages:
> pydoc classtemplate

To try all the tests in doctest (and execute the script):
> python classtemplate.py -v
"""

#Class definition
class Table:
"""Class Table.

Doctest: here we insert python command lines inputs and outputs.
>>> print Table.database
http://access.com/db
"""

#Data attributes here
database='http://access.com/db'

#Method attributes here
def __init__(self,id,text):
"""Initializes the id and textlabel data attributes.

Doctest: Testing more data attributes defined at construction time
>>> x = Table(1,'coucou')
>>> print x.id
1
>>> print x.textlabel
coucou
"""
self.id=id
self.textlabel=text

#doctest -- "Debugging sucks :( Testing rocks :)"
def _test():
"""Inline Doctest activated. Cool! :D
This means that whenever the module is called in python

> python thismodule.py -v

the doctest function will try all the tests implemented in doctest.
"""
import doctest
doctest.testmod()

if __name__ == "__main__":
_test()
</code>

==== The man page ====
Here's the generated documentation

> pydoc classtemplate

Help on module classtemplate:

NAME
classtemplate - A python primer. pydoc, doctest and classes.

FILE
/users/left/guillaume/python/classtemplate.py

DESCRIPTION
Syntax:
To generate man pages:
> pydoc classtemplate

To try all the tests in doctest.
> python classtemplate.py -v

CLASSES
Table

class Table
| Class Table.
|
| Doctest: here we insert python command lines inputs and outputs.
| >>> print Table.database
| http://access.com/db
|
| Methods defined here:
|
| __init__(self, id, text)
| Initializes the id and textlabel data attributes.
|
| Doctest: Testing more data attributes defined at construction time
| >>> x = Table(1,'coucou')
| >>> print x.id
| 1
| >>> print x.textlabel
| coucou
|
| ----------------------------------------------------------------------
| Data and other attributes defined here:
|
| database = 'http://access.com/db'

==== The unittests results ====
Here are the verbose output from the unit-tests (using doctest):
> python classtemplate.py -v

Trying:
print Table.database
Expecting:
http://access.com/db
ok
Trying:
x = Table(1,'coucou')
Expecting nothing
ok
Trying:
print x.id
Expecting:
1
ok
Trying:
print x.textlabel
Expecting:
coucou
ok
2 items had no tests:
__main__
__main__._test
2 items passed all tests:
1 tests in __main__.Table
3 tests in __main__.Table.__init__
4 tests in 4 items.
4 passed and 0 failed.
Test passed.

==Relevant modules for shell-alike scripting==
Here's a list of interesting module for interacting with the OS.
import os # getcwd, chdir
import shutil # file manip utilities: move, copyfile
import glob # file wildcards
import sys # command-line arguments processing, error, stderror redirection
import re # pattern matching, regexp
import math # mathematical functions
import urllib # http addressing. gets and posts method
import smtplib # send emails
import poplib # read emails
from datetime import date # date time manipulations
from timeit import Timer # performance timer
import unittest # unit testing --> agile, eXtreme development
import xmlrpclib # xml get, extract and parse.
from xml.dom import minidom

==Sample code==
'''NOTE: All samples should be corrected with tabulations when performing copy/paste actions!'''

===Celsius===
Transforms fahrenheits degrees into celsius degrees:

#!/usr/bin/python
import string, sys

# If no arguments were given, print a helpful message
if len(sys.argv)==1:
print 'Usage: celsius temp1 temp2 ...'
sys.exit(0)

# Loop over the arguments
for i in sys.argv[1:]:
try:
fahrenheit=float(string.atoi(i))
except string.atoi_error:
print repr(i), "not a numeric value"
else:
celsius=(fahrenheit-32)*5.0/9.0
print '%i\260F = %i\260C' % (int(fahrenheit), int(celsius+.5))

===Twitter===
Gets a list of users in the [[Twitter]] PublicTimeline. Requires the [[Twitter]] Api module.

#!/usr/bin/python
import twitter

api = twitter.Api()
statuses = api.GetPublicTimeline()
print [s.user.name for s in statuses]

===Xspf extract===
<code>[python,Y]
#! /usr/bin/python
""" Scrap mp3 files from xspf playlist
"""
import sys, string, urllib
from xml.dom import minidom

url=sys.argv[1]
feed=urllib.urlopen(url)
#feed=url
xspf=minidom.parse(feed)
locations=xspf.getElementsByTagName('location')
for location in locations:
track_url=string.strip(location.firstChild.data)
print track_url
</code>

==re - Regular Expressions==
===Web-scrapping===
Here are some web-scraping guidelines in Python:

#Here's a generic html code snippet:
In [298]: print string
<description hrel="come here" >Coucou Here <a href="" >I</a> am</description><description hrel="come here" >Coucou Here <a href="" >I</a> am</description>

#Let's isolate the content of ''description'' tags:
In [301]: subtr = re.sub(r'<description.*?>(.*?)</description>',r'\1&',string)
In [302]: print subtr
Coucou Here <a href="" >I</a> am&Coucou Here <a href="" >I</a> am&

#Let's purge the content from html formatting:
In [303]: re.sub(r"<.*?>","",subtr)
Out[303]: 'Coucou Here I am&Coucou Here I am&'

==External References==
*[http://docs.python.org/tut/ Python tutorial],
*[http://en.wikipedia.org/wiki/Python_(programming_language) Python@wikipedia],
*[http://www.scipy.org/ Scientific Python],
*[http://refactormycode.com/codes/51-classtemplate Refactormycode template].

[[Category:Linux]]
[[Category:Python]]
[[Category:Script]]
[[Category:Programming]]

Rails

2008-09-04T15:27:42Z

192.168.20.177:

Rails or [[Ruby]] on Rails is a web-development framework in [[ruby]] that uses the [http://en.wikipedia.org/wiki/Model-view-controller model-view-controller (MVC)] pattern.

==Install==
You need to have ruby and gems installed. Sqlite is also recommended.

> sudo yum install sqlite3 sqlite3-devel
> sudo gem install rails

==Your first rails app==

> rails mywebapp
> cd mywebapp
> script/controller welcome hello
edit, then save, the ''mywebapp/app/views/welcome/hello.html.erb'' ...
> script/server

Open up in your browser ''http://localhost:3000/welcome/hello''. That's it!

==See also==
*[[Ruby]]
*[[Python]]
*[[Perl]]

==External links==
*[http://wiki.rubyonrails.org/rails/pages/Tutorial Rails tutorial]

[[Category:Programming]]

Qrcode

2008-09-03T15:35:19Z

192.168.20.177: /* Python */

[http://en.wikipedia.org/wiki/QR_Code Qrcode] is a non-proprietary encoding of information into 2d codes. 2d codes are bidimensional matrices that encode information much like the traditional barcodes you find in supermarket products. Widely spread in Japan for some years now, it allows users with cameras on their mobile phones to scan the 2d code and extract the information. If it's a hyperlink, then the scanner software may open the phone's web browser and open the hyperlink page.

==Hello world example==

http://farm4.static.flickr.com/3093/2824480513_cb08e32b3b_m.jpg

===Python===
You can easily use the [[python]] library [http://www.pedemonte.eu/wiki/index.php/Documentation:PyQrCodec PyQrCodec] (depends on the [http://www.pythonware.com/products/pil/ PIL] library)

> sudo yum install opencv opencv-devel opencv-python

> wget http://effbot.org/downloads/Imaging-1.1.6.tar.gz
> tar -xvf Imaging-1.1.6.tar.gz
> cd Imaging-1.1.6
> python setup.py build
> sudo python setup.py install

> wget http://www.pedemonte.eu:81/pyqr/files/PyQrcodec_Linux.tar.gz
> tar -xvf PyQrcodec_Linux.tar.gz
> cd PyQrcodec
> python setup.py build
> sudo python setup.py install

<code>[python]
>>> import PyQrCodec
>>> size, image = PyQrCodec.encode("Hello world!")
>>> image.save("helloworld.jpg")
</code>

==External links==
*[http://en.wikipedia.org/wiki/QR_Code QR code in wikipedia]
===Encoders/decoders===
*[http://semapedia.org Semapedia]
*[http://qrcode.kaywa.com/ Kaywa]
*[http://www.neoreader.com/code.html Neoreader]

[[Category:internet]]

Lagged correlation

2008-08-28T10:25:21Z

192.168.20.177: /* Matlab functions */

[[Convolution]] or [[cross-correlation]] are similar operands that can be applied to any square-integrable real functions <mathtex>f</mathtex> and <mathtex>g</mathtex>.

==Convolution==

: <mathtex> \left( f \, * \, g \right)(\tau) \equiv \int_{-\infty}^{\infty} f(t) \, g(\tau-t) \,dt </mathtex>.

==Cross-correlation==

: <mathtex> \left( f \, \star \, g \right)(\tau) \equiv \int_{-\infty}^{\infty} f^{*}(t) \, g(\tau+t) \,dt \equiv C_{fg}(\tau)</mathtex>.

: In particular <mathtex> f \, \star \, f </mathtex> is designated the [http://mathworld.wolfram.com/Autocorrelation.html autocorrelation].

===Normalized===

: <mathtex>\widehat{C}_{fg}(\tau) \equiv \frac{\int_{-\infty}^{\infty} F^{*}(t) \, G(\tau+t) \,dt}{\int_{-\infty}^{\infty} F^{*}(t) \, F(t) \,dt \, \int_{-\infty}^{\infty} G^{*}(t) \, G(t) \,dt} = \left< \frac{F(t)}{\|F\|} ,\, \frac{G(\tau+t)}{\|G\|} \right></mathtex>, where <mathtex> F \equiv f - \overline{f} </mathtex>. The idea is to remove the average and, optionally, other linear or physical trends from <mathtex> f </mathtex>.

: In particular we have

: <mathtex>\widehat{C}_{fg}(0) = \left< \frac{F}{\|F\|} ,\, \frac{G}{\|G\|} \right></mathtex>.

: <mathtex>\widehat{C}_{ff}(0) = 1 </mathtex>.

===Discretized===

: <mathtex>\widehat{C}_{fg}(k) \equiv \frac{1}{n-1} \sum_{i} \frac{ \left( f_i - \overline{f} \right)^{*} \left( g_{k+i} - \overline{g} \right) }{\sigma_f \sigma_g} </mathtex>, where <mathtex>\sigma_f</mathtex> is the variance of <mathtex>f</mathtex>.

: In particular <mathtex> \widehat{C}_{fg}(0) </mathtex> is the famous [http://en.wikipedia.org/wiki/Correlation correlation] coefficient.

==Example==

When both <mathtex>f</mathtex> and <mathtex>g</mathtex> are [http://en.wikipedia.org/wiki/Even_and_odd_functions even] functions then the [[convolution]] and [[cross-correlation]] products are rigorously equivalent. Below, we show these products when applied to box functions (left figure) and to gaussian functions (right figure). In both cases, they are [http://en.wikipedia.org/wiki/Even_and_odd_functions even] functions. <mathtex>f</mathtex> is represented by the red line, <mathtex>g</mathtex> is represented by the blue line, the product <mathtex>f(t) \, g(\tau - t)</mathtex> is represented by the solid blue line. The solid blue area is the convolution product for lag-time <mathtex>\tau</mathtex> and the whole convolution product function (for all <mathtex>\tau</mathtex>) is represented by the green line.

http://mathworld.wolfram.com/images/gifs/convrect.gif http://mathworld.wolfram.com/images/gifs/convgaus.gif

The big conclusions we can make is that if <mathtex>f</mathtex> and <mathtex>g</mathtex> are the same functions, but with a lag of <mathtex>\epsilon</mathtex> between them, then the [[cross-correlation]] product is maximum when <mathtex>\tau = \epsilon</mathtex>.

==Matlab functions==

===xcorr===
Calculates the cross correlation from two signals.

%Consider arrays t, y1(t), y2(t)
N=length(t);
tlag = linspace(-t(N/2), t(N/2), N+1);
crosscorr = xcorr( y1, y2, N/2, 'coeff');
plot(tlag,crosscorr); xlabel('Phase in time units');ylabel('coefficient');

===cpsd===
Calculates the cross power spectral density (PSD) function of signals <mathtex> x(t)</mathtex> and <mathtex> y(t)</mathtex>.

===periodogram or pwelch===
Calculates the power spectral density (PSD) function of signal <mathtex> x(t)</mathtex>. The [[#periodogram|periodogram]] may use several window functions as option. The [[#pwelch|pwelch]] will use the welch window.

===mscoherence===
Calculates the coherence-squared spectrum function. If you apply an inverse Fourier transform (IFT), then you get the cross-correlation function in a very efficient way.

==See also==
*[http://mathworld.wolfram.com/Cross-Correlation.html Cross-correlation in MathWorld],
*[http://mathworld.wolfram.com/Convolution.html Convolution in MathWorld],
*[http://en.wikipedia.org/wiki/Phase_correlation Phase correlation on Wikipedia]

Fes2004

2008-08-27T09:11:50Z

192.168.20.177: /* Building fes2004 from scratch under windows */

Fes2004 is the tide level and harmonic predictor for tide of POC-LEGOS. Development credits go to Thierry Letellier and Florent Lyard.

An open discussion started around [http://www.mohid.com/hydrogroup/presentations/HG_060419_fes2004.ppt this] presentation.

== TODOs ==
#Include in Mohid the new tide components missing in fes95.
#Make simple tests close to the coast and far away from the coast. Compare them with fes95.
#Update this wiki.

== Quick start ==
Get the [http://maretec.mohid.com/PublicData/products/Software/Mohid-Tide_v0.4.zip package]. Unpack it and read the readme-1st file for instructions. If you're working within [[MARETEC]] or [[HIDROMOD]] then map a network drive (say, ''X:'') to ''\\kepler\DataCenter1\DataCenter\Modelos_2(2)\FES\fes2004data''. If not, get the datasets [http://www.aviso.oceanobs.com/en/data/products/auxiliary-products/global-tide-fes2004-fes99/index.html fes2004 here] and install them somewhere in your network with read permissions.

=== Mohid-tide ===
Here's what the input file should look like (CAUTION: it's longitude latitude null!):
CAUTION: The file MUST END with <end_xyz>! Otherwise results will be erroneous. NO BLANK LINES ARE ALLOWED!
longitude latitude null
*Sample input:
<begin_xyz>
-61.410 -38.995 0.
-61.41 -39.00 0.
-61.41001 -38.99 0.
-61.41001 -38.7 0.
-61.41 -39.38 0.
-70.2 -56.2 0.
<end_xyz>
*The command line is :
mohid-tide X:\tide.nc input_mohid-tide.dat output.dat 0 2.08
In this example, the input file is called ''input_mohid-tide.dat''. The output file is called ''output.dat''. The data file is called ''tide.nc'' and it's path is ''X:\''. The ''0'' and the ''2.08'' are respectively the time reference and the water level reference. Change all these parameters accordingly to your situation.
*Sample output
<begingauge>
NAME : nth test
LONGITUDE : -7.00000 49.0000 51.0000
LATITUDE : 33.0000 35.0000 26.0000
METRIC_X : -7.83090
METRIC_Y : 33.5906
REF_LEVEL : 2.08000
TIME_REF : 0.000000
M2 : 0.996598 52.7018
S2 : 0.350935 77.8265
K1 : 0.0661576 49.9613
K2 : 0.0950913 71.3380
N2 : 0.214260 36.6291
2N2 : 0.0317467 16.2234
O1 : 0.0591364 -50.3478
Q1 : 0.0218185 49.4025
P1 : 0.0182365 -99.5383
M4 : 0.000000 0.000000
Mf : 0.00237638 -7.58905
Mm : 0.000951622 -38.4179
Mtm : 0.000819045 24.8848
MSqm : 0.000119478 33.8243
<endgauge>

== Building fes2004 from scratch under windows ==

=== Prerequisites ===

#Get the [http://www6.in.tum.de/~kiss/WinGsl.htm WinGSL] distribution. Unpack at least the dll.
#Get the [http://www.unidata.ucar.edu/downloads/netcdf/ftp/contrib/win32/netcdf-3.6.1-win32.zip netcdf] distribution. Unpack at least the dll.
#Get the [http://www.legos.obs-mip.fr/en/soa/cgi/getarc/v0.0/index.pl.cgi?donnees=maree&produit=modele_fes fes2004 distribution].
#Get the [ftp://ftp.legos.obs-mip.fr/pub/soa/maree/tide_model/global_solution/fes2004/tide/tide.fes2004.nc data] file(~600MB) and rename it to tide.nc (or get it at ''\\kepler\DataCenter1\DataCenter\Modelos_2(2)\FES\fes2004data'').

== fes2004 vs fes95 ==
Essentially fes2004 contains 4 new relevant tidal components. And it supports higher resolution,
allowing extraction of tidal gauges closer to the coast. These two reasons alone make it a very interesting asset to include in Mohid.

== Documents ==
#Kick start [http://www.mohid.com/hydrogroup/presentations/HG_060419_fes2004.ppt powerpoint].
#Reference [http://www.springerlink.com/content/j8v764349t7j4523/ paper] for the Fes2004 solution.
#Beta-version [http://maretec.mohid.com/PublicData/products/Software/Mohid-Tide_v0.4.zip package].
#Guillaume's project at '''\\guillaume\projectos\fes2004'''
#The [ftp://ftp.legos.obs-mip.fr/pub/soa/maree/tide_model/global_solution/fes2004/tide/tide.fes2004.nc data] file (~600MB) or you can get at ''\\kepler\DataCenter1\DataCenter\Modelos_2(2)\FES\fes2004data''.

==Related links==
*[[MatLab_TideAnalyser]]

[[Category:Tools]]

Cross-correlation

2008-08-20T13:23:15Z

192.168.20.177:

#REDIRECT[[Lagged correlation]]

Convolution

2008-08-20T13:21:30Z

192.168.20.177:

#REDIRECT[[Cross-correlation]]

Geometry diagnostic

2008-08-01T10:22:08Z

192.168.20.177: /* LowerLayer */

Once the vertical discretization or [[Module Geometry|geometry]] is imposed and the bathymetry is chosen, the bottom layer can yield stability problems when using shaved cells. You can have very thin bottom cell next to a very wide bottom cell. To diagnose the existence of such problematic cells, a [[geometry diagnostic]] tool was developed.

==Source-safe whereabouts==
The latest source code is in the '''Mohid_V4''' repository, inside the '''small tools\GeometryDiagnostic''' folder.

==Configuration==

The inputs required are a bathymetry [[Grid Data|grid data]] file, a [[Module Geometry|geometry]] file, an hdf5 output filename and a [[Grid Data|grid data]] output filename.

===Nomfich.dat===

IN_MODEL : GeometryDiagnostics.dat

===GeometryDiagnostics.dat===

BATIM : Biscay_Level2__.new2
GEOMETRY : D:\Aplica\BiscayAplica\GeneralData\Ocean\Geometry\Level2\Geometry.dat
OUT_FILE : geomdiag_new2.hdf5
OUT_GRIDDATA3D : geomdiag_new2.dat

== Outputs ==
The outputs are an hdf5 file and a three-dimensional [[Grid Data|grid data]] file.

<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/0522d989-f1b1-4475-8496-38d8f66356df/2008-08-01_1102.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/0522d989-f1b1-4475-8496-38d8f66356df/2008-08-01_1102.png" width="633" height="428" border="0" /></a>
</htm>

===LowerLayerThickness===

For all horizontal cells ''i'', ''j'', there is one bottom layer ''kbottom'' that defines the bottom layer thickness ''DWZ(i, j, kbottom)''; where ''DWZ'' is the 3D matrix that defines the layers thickness for every water column.

LowerLayerThickness(i,j) = DWZ(i,j, kbottom)

<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/86accff2-ee8e-4a6a-8056-59e73a0aec22/2008-08-01_1115.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/86accff2-ee8e-4a6a-8056-59e73a0aec22/2008-08-01_1115.png" width="562" height="426" border="0" /></a>
</htm>

===LowerLayerThicknessGradU===
Is the ratio of neighboring cells bottom layer thickness along the X axis.

aux = DWZ(i,j, kbottom)/DWZ(i,j-1, kbottom)
LowerLayerThicknessGradU(i,j) = min( aux, 1/aux)

===LowerLayerThicknessGradV===
Is the ratio of neighboring cells bottom layer thickness along the Y axis.

aux = DWZ(i,j, kbottom)/DWZ(i-1,j, kbottom)
LowerLayerThicknessGradV(i,j) = min( aux, 1/aux)

==See also==
*[[Module Geometry]]

[[Category: Tools]]

DrawFluxesInHDF5

2008-08-01T10:10:57Z

192.168.20.177:

[[DrawFluxesInHDF5]] is a little tool that reads the boxes fluxes time series (.BXF and .BXM) and returns an HDF5 file with vector fields representing the fluxes between the boxes.

==Source-safe whereabouts==
The latest source code is in the '''Mohid_V4''' repository, inside the '''SmallTools\DrawFluxesInHDF5''' folder.

==Configuration==

===Nomfich.dat===
The nomfich file contains a single line pointing to the configuration file.
IN_MODEL : CreateHDF5Boxes.dat

===CreateHDF5Boxes.dat===
Here's a sample configuration file (CreateHDF5Boxes.dat):

HDF5BOXES_INFILE : Boxes.hdf5
HDF5BOXES_OUFILE : OutBoxes.hdf5
BOXESSALINITYFILE : salinity.bxm
BOXESWATERFILE : water.bxm
BOXESWATERFLUXFILE : water.bxf
INDEXESFILE : BoxesFluxesIndexes.txt
INDEXESLENGTH : 436

# The first line contains the input boxes.hdf5 file. They represent the index map of the boxes created with the [[BoxHDF5]] tool.
# The second line tells the output filename.
# The third line contains the salinity inside the boxes.
# The fourth line contains the boxes water volumes timeseries.
# The fifth line contains the fluxes between boxes timeseries.
# The sixth line contains three columns displaying the column number, the source box index and the destination box index. Each row represents a flux of the water fluxes timeseries.
# The seventh and last line contains the total number of fluxes available in the water fluxes timeseries.

==BoxesFluxesIndexes.txt==
Here's a sample of the indexes file:
9 1 2
10 2 3
11 5 6
12 6 7
13 6 38
14 7 1
15 7 8
16 7 39
17 8 2
18 8 9
19 8 40
20 9 3
# First column: column index number.
# Second column: source box index.
# Third column: target box index.

==Example output==
<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/9a4a7e12-6de7-4ca9-b5e2-5537f9679bd2/2008-07-25_1746.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/9a4a7e12-6de7-4ca9-b5e2-5537f9679bd2/2008-07-25_1746.png" width="500" height="400" border="0" /></a>
</htm>

==Troubleshoot==
'''Q: Too many columns?'''

A: Add the following preprocessor directives in Module [[Mohid Base 1]]:
_BIG_MAX_COLUMNS,_EXTRA_LONG_LINE_LENGTH

==See also==
*[[Boxes]]

[[Category:Mohid]]
[[Category:Tools]]

Module Geometry

2008-08-01T09:43:19Z

192.168.20.177:

== Overview ==
Module Geometry handles the vertical discretization in MOHID. It was designed to divide the water column (in MOHID Water) or the soil compartment (in MOHID Land) in different vertical coordinates: Sigma, Cartesian, Lagrangian, Fixed Spacing, Harmonic, etc. A subdivision of the vertical domain into different sub-domains using different vertical coordinate systems is also possible.

== General options ==
*Minimum depth

== Vertical coordinate system ==

=== Sigma ===
[[Image:SZZ.gif|center|425px|thumb|Vertical sigma mesh]]

=== Cartesian ===
The Cartesian coordinate can be used with or without [[shaved cells]].

=== Fixspacing ===
The [[Fixed Spacing coordinates|Fixed Spacing]] coordinate allows the user to study flows close to the bottom.

=== Lagrangian ===
The [[Lagrangian coordinate]] moves the upper and lower faces with the vertical flow velocity.

=== Harmonic ===
The Harmonic coordinate works like the Cartesian coordinate, just that the horizontal faces close to the surface expand and collapse depending on the variation of the surface elevation. This coordinate was implemented in the geometry module to simulate reservoirs.

=== Fixsediment ===

=== SigmaTop ===

=== Cartesiantop ===

== Distances ==
[[Image:Mohid_distances.JPG|center|250px|thumb|MOHID syntax for distances]]
===Public routines===
; ModuleHorizontalGrid: GetHorizontalGrid(HorizontalGridID, XX_IE, YY_IE, XX_Z, YY_Z,XX_U, YY_U, XX_V, YY_V, XX_Cross, YY_Cross, DXX, DYY, DZX, DZY, DUX, DUY, DVX, DVY, XX, YY, XX2D_Z, YY2D_Z, STAT)
; ModuleGeometry: GetGeometryDistances(GeometryID, SZZ, DZZ, DWZ, DUZ, DVZ, DZI, DZE,ZCellCenter, ActualTime, STAT)

== Areas ==

== Volumes ==
[[Image:VolumeDeControlo.gif|center|250px|thumb|Single T-cell control volume]]

<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png" width="544" height="191" border="0" /></a>
</htm>

== Bathymetry consistency diagnostic ==

Once the vertical discretization is imposed and the bathymetry is chosen, the bottom layer can yield stability problems when using shaved cells. You can have very thin bottom cell next to a very wide bottom cell. To diagnose the existence of such problematic cells, a [[geometry diagnostic]] tool was developed.

[[Category:Modules]]
[[Category:MOHID Base 2]]

== Input data file ==

Energy

2008-07-31T18:50:17Z

192.168.20.177:

[[Energy]] calculates a domain averaged timeseries of the following diagnostic properties:

;Kinetic energy : is the mass with squared velocity modulus product integration.

;Potential energy : is the mass with gravitic constant and hydrographic zero distance product integration.

;Enstrophy : Is the squared velocity curl integral.

; Volume : is the integral of all wet [[Module_Geometry#Volumes|T-cells]] volumes.

;Mass : is the density with [[Module_Geometry#Volumes|T-cells]] volume product integration.

The diagnostic properties computation can be found in the routine '''ComputeSystemEnergy''' inside the [[Module Hydrodynamic]]. All the properties were interpolated to type [[Module_Geometry#Volumes|T-Cells]].

==Usage==

Energy: 1

==See also==
*[[Module Hydrodynamic]]

[[Category:MOHID Water]]

ImposedSolution

2008-07-31T17:16:52Z

192.168.20.177:

The idea behind the imposed solution, is the ability to run lagrangian tracers in offline mode. But it can also be used to calculate [[Residual|residual fields]] of velocity and water level, as well as the [[Energy|energy]] timeserie, given hydrodynamics and waterproperties from hdf5 files.

==Sample configuration==

==See also==
*[[Evolution]]

[[Category:MOHID Water]]

Evolution

2008-07-31T17:00:53Z

192.168.20.177: /* External links */

There are several ways of running MOHID water hydrodynamics. The keyword that controls these several ways is [[Evolution|EVOLUTION]] from the [[module Hydrodynamic]] file.

Here's the list of possible options for this keyword:

#[[Solve_Equations]] : Default value, it solves the Primitive Ocean Equations.
#[[Read_File]] : Reads the solution from a file
#[[No_hydrodynamic]] : Doesn't calculates the hydrodynamic at all
#[[Residual_hydrodynamic]] : ??
#[[Run_Off]] : ??
#[[ImposedSolution]] : Uses a reference solution for U, V and level.
#[[Vertical1D]] : Used when modelling a simple 1D vertical model. It takes into account the Ekman spiral, provided the model is forced with wind stress at the surface, or with friction at the bottom.

==Example ==

EVOLUTION : [[Vertical1D]]

==External links==
*[http://www.mohid.com/IHS Mohid Keywords database]

[[Category:MOHID Water]]

2gif

2008-07-29T15:01:41Z

192.168.20.177: /* Make colors transparent */

[[2gif]] is a nice little utility used to create gif animations.

==Syntax==
Please put the executable directory in the <code>PATH</code> environment variable.

The following syntax allows to create an animated gif ''anim.gif'' from ''bmp'' files with a delay of 500 ms between each frame:
$ 2gif.exe s=*.bmp -namegen=anim.gif -unite -Delay500

== Make colors transparent ==

$ 2gif.exe s="C:\Source Images\*.*" d="C:\out" -totranspm(255,255,255)

== Command line tips ==
Producing large amounts of snapshots and creating animations can be very time-consuming. Here are a few tips for speeding up with the commandline:
*Get the [[2gif]] utility and add the folder to the ''PATH'' environment variable.
*Get the ''winzip'' utility and add the folder to the ''PATH'' environment variable.
The idea is basically inside your figures folder, to create a subfolder with the number of the run, and save inside the images and animations. The goal is to keep the same structure for each run, thus allowing more efficiency.

Open a command line window and go to the figures folder:
$ xcopy /T /E Run_1 Run_New
$ cd Run_New
Now create a snapshot of the results, and save the images and the animation
$ 2gif.exe s=*.bmp -namegen=anim.gif -unite -Delay1000
$ winzip32 -min -m images.zip *.bmp
$ move *.* This_snap

==Useful references==
*[[2eps]]
*[[Convert]]
*[[Jpeg2ps]]
*[[Winzip]]
*[[2jpeg]]

Boxes

2008-07-24T14:55:48Z

192.168.20.177:

== Overview ==
A box file is used to define an area, which can be 2D or 3D. These areas can be used to initialize properties fields or integrate values in time and space inside and between boxes, allowing computing global and zonal budgets for almost every modeled variables. [[Module BoxDif]] is the module responsible for handling and interpreting the boxes files.

== Boxes file ==
Boxes files can be automatically generated by [[Mohid_GIS#Create_Boxes|MOHID GIS]] based on a [[bathymetry]] file and on a [[polygon]] file.

A box file requires the definition polygons. These polygons are defined by vertices indicated by the grid cell [i,j] indexes. Thus, a box file is always specific of a certain [[grid]] file. Please note that in [[polygon]] files, used in MOHID GIS, the polygon vertices are defined by real coordinates [x,y].

In a box file, several boxes can be defined. An ID number is given to each box, based on the order in which the box file is read. Box 1 is the first block in the file, Box 2 the second and so on. By default a Box 0 (zero) is always created, corresponding to the box containing all the grid points that were not included inside the boxes. This way if box integration is requested and no boxes are defined, the output will be the integration of the entire domain.

When used to integrate values, the correspondent outputs are written in [[Time Series]] format. Thus, in the box file needs information on the time step to write results, which is given by keyword:

DT_OUTPUT_TIME : 3600

As a safety feature, a [[Grid Data]] file can be written in the beginning of a simulation, where in to each grid cell, the index of the corresponding box is written. This can be done by defining keyword:

WRITE_BOXES : 1

and then the name of the output file to be written:

OUTPUT_FILE : ..\GeneralData\Boxes\BoxesFileInGridDataFormat.dat

== Sample ==
This example shows the definition of a box with 4 vertices. By default [[Module BoxDif]] automatically introduces an extra vertice at the end of the list which is equal to the first vertex, thus insuring the polygon is closed.

=== 2D box file ===

DT_OUTPUT_TIME : 3600
WRITE_BOXES : 0

'''<beginpolygon>'''
<<beginvertix>>
44 39
33 77
71 88
82 49
<<endvertix>>
'''<endpolygon>

=== 3D box file ===
This example shows the definition of two boxes, defined by the same polygon, but which integrate in the vertical direction, from layer 1 to 5, and from layer 6 to 10.

DT_OUTPUT_TIME : 3600
WRITE_BOXES : 0

'''<beginpolygon>'''
<<beginvertix>>
44 39
33 77
71 88
82 49
<<endvertix>>
<<beginverticallayer>>
1 5
6 10
<<endverticallayer>>
'''<endpolygon>'''

==See also==
*[[DrawFluxesInHDF5]]

[[Category:Input Data Formats]]

Matlab

2008-07-08T18:25:11Z

192.168.20.177: /* How to run matlab from the command line? */

MATLAB is a numerical computing environment and programming language. Created by the [http://www.mathworks.com MathWorks], MATLAB allows easy matrix manipulation, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs in other languages.

== How to install Matlab from IST ? ==
Go to [https://delta.ist.utl.pt/software/matlab.php delta.ist.utl.pt] and follow the instructions there. You should obtain the license files in your email after you fill up a form.

== MOHID and MATLAB ==
Since release 7.4(R2007a) it supports reading and writing MOHID [[HDF5]] files.

There are [[Mohid_Support_Tools#MatLab_Tools|several tools]] available to [[MOHID]] users and developers in the [[SourceSafe]] database "OtherTools/MatLab". Detailed information of these tools can be found [[Mohid_Support_Tools#MatLab_Tools|here]]

== How to run matlab from the command line? ==
Make sure you end the script you want to invoke from the command line with ''exit'' (type ''help exit'' at the matlab prompt then add ''exit'' as the last line in the script).

=== Windows ===
Assuming ''script.m'' is a valid matlab script that finishes with the ''exit'' command, typing from the dos command line
$ matlab -r script(arguments)
will open matlab, execute the script and then exit matlab.

New version of Matlab needs the ''-wait'' option, otherwise it may not function properly in batchfiles:
$ matlab -r -wait script(arguments)

=== Unix ===
To run matlab in text mode only type:
> matlab -nodesktop -nojvm -nodisplay

To run matlab in background type:
> nohup matlab -nodesktop -nojvm (-nodisplay) < script.m > _matlab.log &
This last line will run matlab in background, execute ''script.m'' and kill the matlab process.

== [[Netcdf]] package ==

===install===
==== Windows ====
===== R2007a and R2007b =====
This installation is described only for the R2007a to R2007b versions of Matlab:
*Prerequisites:
**[http://mexcdf.sourceforge.net/downloads/ mexnc R2007a or R2007b]
**[http://mexcdf.sourceforge.net/downloads/ snctools], (here for [[snctools]] wiki article),
**[http://www.eos.ubc.ca/~rich/private/mapug.html m_map]
*Steps:
*#Download all the above packages,
*#Transfer the netcdf.dll shipped with mexnc to the windows system path,
*#Add in the matlab path setup the paths to mexnc,
*#Save and restart matlab,
*#Open Matlab,
*#[OPTIONAL]: to enable opendap, you must install the netcdf [ftp://ftp.unidata.ucar.edu/pub/netcdf-java/v4.0/ toolsUI jar file]. Installation instructions are available [http://mexcdf.sourceforge.net/tutorial/ch02.html here].
*#[OPTIONAL]: add the path and filename of toolsUI jar file in the classpath.txt in the /toolbox/local directory of your matlab installation,
*#Go to the tests folder in snctools and launch test_snctools.m,
*#That's it!
For the m_map package instructions go to http://www.eos.ubc.ca/~rich/private/mapug.html. For the high-res coastline and bathymetry datasets goto http://www.eos.ubc.ca/~rich/private/mapug.html#p9.

NOTE: You can check http://mexcdf.sourceforge.net/tutorial/ch02.html for a quick alternative netcdf installation...

NOTE: If the following error occurs, make sure you have installed the netcdf.dll file, shipped with mexnc, in your windows system path:
??? Invalid MEX-file

=====R12 to R14=====
This installation is described only for the R12 to R14 versions of Matlab:
*Prerequisites:
**[http://www.opendap.org/download/libdap++.html libdap-prerequisites3.7.3]
**[http://www.opendap.org/download/ml-structs.html ml-structs]
**[http://mexcdf.sourceforge.net/downloads/ mexnc R14 or R12]
**[http://www.marine.csiro.au/sw/matlab-netcdf.html#Installation matlab_netCDF_OPeNDAP]
**[http://www.eos.ubc.ca/~rich/private/mapug.html m_map]
*Steps:
*#Download all the above packages,
*#Copy the dll files from libdap-prerequisites3.7.3 to the ml-structs folder.
*#Add in the matlab path setup the paths to ml-structs, matlab_netCDF_OPeNDAP and mexnc R14 or R12,
*#Save and restart matlab,
*#Open Matlab, go to the tests folder in mexnc R14 or R12 and launch test_mexnc.m,
*#Next, go to the tests folder in matlab_netCDF_OPeNDAP and launch test_all.m,
*#That's it!
Check out this page for more detailed instructions: http://www.marine.csiro.au/sw/matlab-netcdf.html. For the m_map package instructions go to http://www.eos.ubc.ca/~rich/private/mapug.html. For the high-res coastline and bathymetry datasets goto http://www.eos.ubc.ca/~rich/private/mapug.html#p9.

NOTE: If using Matlab R13, then use the mexnc R12 release and not the mexnc R14 release!

NOTE: If the following error occur during the test_all.m, then edit the compare_mats_getnc.m file at line 45 and replace {} with (). Rerun the test_all.m. That should do it!
Error: File: C:\MATLAB6p5\toolbox\matlab_netCDF_OPeNDAP\test\compare_mats_getnc.m Line: 45 Column: 59
Functions cannot be indexed using {} or . indexing.

NOTE: If the following error occurs, make sure you have installed the netcdf.dll file, shipped with mexnc, in your windows system path:
??? Invalid MEX-file

==== Unix ====
*To install the netcdf package you first require to install the netcdf libraries. Get the latest ''netcdf.tar.gz'' and unpack them in a temporary directory. Then type:
> ./configure --enable-fortran (--enable-64) --prefix=/usr/local/netcdf --exec-prefix=/usr/local/netcdf
Next edit the ''macros.make'' file and add the ''-fpic'' option to both ''CFLAGS'' and ''CXXFLAGS''
> vim macros.make
CFLAGS = -g -O2 -fpic
CXXFLAGS = -g -O2 -fpic
Then type make
> make
> sudo make install
This will install the netcdf libraries in the <code>/usr/local/netcdf</code> directory.

*Next, get the latest ''mexnc.tar.gz'' files and unpack them the ''matlab/toolbox'' temporary directory. Then copy the <code>mexopts.sh</code> file from the matlab root directory into the temporary directory and add the following lines at the end:

#############################################################################
#
# Architecture independent lines:
#
# Set and uncomment any lines which will apply to all architectures.
#
#----------------------------------------------------------------------------
NETCDF="/usr/local/netcdf"
EXTRA_CFLAGS="-I${NETCDF}/include"
EXTRA_CLIBS="-L${NETCDF}/lib -lnetcdf "
CFLAGS="-g $CFLAGS ${EXTRA_CFLAGS}"
CLIBS="$CLIBS ${EXTRA_CLIBS} "
#----------------------------------------------------------------------------
#############################################################################
Then run make:
> make
Finally add the ''matlab/toolbox/mexnc'' path to the matlab environment.

*Continuing, to have opendap accessible installation of the opendap client libraries is required:
> yum install libdap
> yum install libnc-dap

===Usage===
==== [[snctools]] ====

===== nc_dump =====
NC_DUMP: a Matlab counterpart to the NetCDF utility 'ncdump'.
NC_DUMP(NCFILE) prints metadata about the netCDF file NCFILE.
NC_DUMP(NCFILE,VARNAME) prints metadata about just the one netCDF variable
named VARNAME.

===== nc_varget =====
NC_VARGET: Retrieve data from a netCDF variable.

DATA = NC_VARGET(NCFILE,VARNAME) retrieves all the data from the
variable VARNAME in the netCDF file NCFILE.

DATA = NC_VARGET(NCFILE,VARNAME,START,COUNT) retrieves the contiguous
portion of the variable specified by the index vectors START and
COUNT. Remember that SNCTOOLS indexing is zero-based, not
one-based. Specifying a -1 in COUNT means to retrieve everything
along that dimension from the START coordinate.

DATA = NC_VARGET(NCFILE,VARNAME,START,COUNT,STRIDE) retrieves
a non-contiguous portion of the dataset. The amount of
skipping along each dimension is given through the STRIDE vector.

NCFILE can also be an OPeNDAP URL if the proper SNCTOOLS backend is
installed. See the README for details.

NC_VARGET tries to be intelligent about retrieving the data.
Since most general matlab operations are done in double precision,
retrieved numeric data will be cast to double precision, while
character data remains just character data.

Singleton dimensions are removed from the output data.

A '_FillValue' attribute is honored by flagging those datums as NaN.
A 'missing_value' attribute is honored by flagging those datums as
NaN. The exception to this is for NC_CHAR variables, as mixing
character data and NaN doesn't really seem to work in matlab.

If the named NetCDF variable has valid scale_factor and add_offset
attributes, then the data is scaled accordingly.

EXAMPLE:
#1. In this case, the variable in question has rank 2, and has size
500x700. We want to retrieve starting at row 300, column 250.
We want 100 contiguous rows, 200 contiguous columns.

vardata = nc_varget ( file, variable_name, [300 250], [100 200] );

==== <strike>getnc</strike> ====
> values = getnc(file, varid, -1, -1, -1, -1, change_miss, new_miss);

> x.file = 'fred.nc';
> x.varid = 'foo';
> x.change_miss = 1;
> values = getnc(x);

==See also==
*[[Matlab samples]]
*[[Netcdf]]
*[[OpenDAP]]

==External References==
*[https://delta.ist.utl.pt/software/matlab.php Matlab @ delta.ist.utl.pt]
*[http://www.mathworks.com MathWorks],
*[http://www.bme.utexas.edu/research/informatics/policies2/topic.aspx?topicid=5#111 matlab from command line],
*[http://www.egr.msu.edu/decs/facilities/software/matlab.php#Background Matlab in background],
*[http://www.stanford.edu/~jichien/matlab.html Matlab in background 2].

[[Category:Tools]]
[[Category:Windows]]
[[Category:Linux]]
[[Category:Technology]]
[[Category:Matlab]]
[[Category:Netcdf]]

Matlab samples

2008-07-08T09:14:53Z

192.168.20.177: /* Read and write netcdf files */

This article compiles some useful [[matlab]] samples to use with the MOHID converted [[netcdf]] files.

==Netcdf MOHID vector plot==
Sample code for the Portuguese coast application. It integrates several layers of the horizontal velocity. And plots and saves it.

file='F:\Results200606\20060601_Hydrodynamic_1.nc';
nc_dump(file)

lon = nc_varget(file,'lon')
lat = nc_varget(file,'lat')
depth = nc_varget(file,'depth')

siz = [length(lon)-1 length(lat)-1];
lon2d = zeros(siz);
lat2d = zeros(siz);

for i=1:siz(1)
for j=1:siz(2)
lon2d(i,j) = lon(i);
lat2d(i,j) = lat(j);
end
end

SumVelX = 0;
SumVelY = 0;

for k=35:42

Vel_xk = nc_varget(file,'Vel_X',[k 1 1],[1 116 176]);
SumVelX = SumVelX + Vel_xk * (depth(k+1) - depth(k)) / (depth(43) - depth(36));

Vel_yk = nc_varget(file,'Vel_Y',[k 1 1],[1 116 176]);
SumVelY = SumVelY + Vel_yk * (depth(k+1) - depth(k)) / (depth(43) - depth(36));

end

%plot arrows
m_proj('miller', 'lon', [min(lon) max(lon)], 'lat', [min(lat) max(lat)]);
m_quiver(lon2d(1:3:end), lat2d(1:3:end), Vel_xk(1:3:end), Vel_yk(1:3:end), 0, 'k');
hold on;
m_grid('box','fancy','linestyle','none','fontsize', 7);
m_usercoast('[http://www.mohid.com/HydroGroup/data_sources/coastline.mat coastline.mat]','patch', [.5 .5 .5]);
%plot scale
m_quiver(-8.5, 37.5, .1, 0.0, 0, 'k');
htv5 = text(.015, .69, '10 cm s^{-1}');
set(htv5,'FontSize',8);

%save figure as a png file
saveas(gcf, 'MyArrowsFigure.png', 'png');

==Read and write netcdf files==

%Read level2 residual fields
%%%%%%%%%%%% 3D results %%%%%%%%%%%%%%%%%%%%%
file = 'BiscayResidual.nc';
u = nc_varget(file,'Vel_X');
v = nc_varget(file,'Vel_Y');
lon = nc_varget(file,'lon');
lat = nc_varget(file, 'lat');
depth = nc_varget(file, 'depth');
level = nc_varget(file, 'Lev_Z');

%Create level1 residual fields
out = 'MOHIDresidual3D.nc';
nc_create_empty(out, nc_write_mode);
nc_add_dimension(out, 'lon', length(lon));
nc_add_dimension(out, 'lat', length(lat));
nc_add_dimension(out, 'deptht', length(depth));

s_ncvars = struct ( 'Name', ...
{ 'lon',...
'lat',...
'deptht',...
'u',...
'v',...
'elevation'}, ...
'Nctype', ...
{ 'float',...
'float',...
'float',...
'float',...
'float',...
'float'}, ...
'Dimension', ...
{ {'lon'},...
{'lat'},...
{'deptht'},...
{'deptht' 'lat' 'lon'},...
{'deptht' 'lat' 'lon'},...
{'lat' 'lon'}}, ...
'Attribute', ...
{ struct( 'Name','units',...
'Value','degrees_east' ), ...
struct( 'Name','units',...
'Value','degrees_north' ), ...
struct( 'Name','units',...
'Value','m' ), ...
struct( 'Name','units',...
'Value','m s-1' ), ...
struct( 'Name','units',...
'Value','m s-1' ), ...
struct( 'Name','units',...
'Value','m' ), ...
})

for i=1:length(s_ncvars)
nc_addvar(out, s_ncvars(i));
end

nc_dump(out);

==See also==
*[[Matlab]]

[[Category:Matlab]]

Polynomial interpolation

2008-06-27T10:52:07Z

192.168.20.177: /* <mathtex>p</mathtex>-th derivative of polynomial interpolation of real function <mathtex>f</mathtex> */

Given <mathtex>n</mathtex> nodes of known values of any real function <mathtex>f</mathtex>, the '''unisolvence theorem''' states that there exists a unique polynomial of degree <mathtex>n-1</mathtex> that interpolates the nodes. Such a polynomial <mathtex>P</mathtex> is easily constructed for low degrees and is easily generalized to any degree.

==Polynomial interpolation of real function <mathtex>f</mathtex>==
By increasing degree:
* <mathtex>P^{1}(x) = f(x_1) \frac{ \left( x - x_2 \right) }{ \left( x_1 - x_2 \right) } + f(x_2) \frac{ \left( x - x_1 \right) }{ \left( x_2 - x_1 \right) } </mathtex>
* <mathtex>P^{2}(x) = f(x_1) \frac{ \left( x - x_2 \right) \left( x - x_3 \right) }{ \left( x_1 - x_2 \right) \left( x_1 - x_3 \right)} + f(x_2) \frac{ \left( x - x_1 \right) \left( x - x_3 \right) }{ \left( x_2 - x_1 \right) \left( x_2 - x_3 \right) } + f(x_3) \frac{ \left( x - x_1 \right) \left( x - x_2 \right) }{ \left( x_3 - x_1 \right) \left( x_3 - x_2 \right) } </mathtex>
* ...
* <mathtex>P^{n-1}(x) = \sum_{i=1}^{n} \frac{ f(x_i) \prod_{j \neq i}^n \left( x - x_j \right) }{ \prod_{j \neq i}^n \left( x_i - x_j \right) } </mathtex>

Where <mathtex>x_1,\, x_2,\, \ldots \, x_n,</mathtex> are the nodes where <mathtex>f</mathtex> is known.

==<mathtex>p</mathtex>-th derivative of polynomial interpolation of real function <mathtex>f</mathtex>==

* <mathtex>P^{1}(x)^{(1)} = f(x_1) \frac{ 1 }{ \left( x_1 - x_2 \right) } + f(x_2) \frac{ 1 }{ \left( x_2 - x_1 \right) } </mathtex>
* <mathtex>P^{2}(x)^{(1)} = f(x_1) \frac{ \left( x - x_2 \right) + \left( x - x_3 \right) }{ \left( x_1 - x_2 \right) \left( x_1 - x_3 \right)} + f(x_2) \frac{ \left( x - x_1 \right) + \left( x - x_3 \right) }{ \left( x_2 - x_1 \right) \left( x_2 - x_3 \right) } + f(x_3) \frac{ \left( x - x_1 \right) + \left( x - x_2 \right) }{ \left( x_3 - x_1 \right) \left( x_3 - x_2 \right) } </mathtex>
* <mathtex>P^{2}(x)^{(2)} = f(x_1) \frac{ 2 }{ \left( x_1 - x_2 \right) \left( x_1 - x_3 \right)} + f(x_2) \frac{ 2 }{ \left( x_2 - x_1 \right) \left( x_2 - x_3 \right) } + f(x_3) \frac{ 2 }{ \left( x_3 - x_1 \right) \left( x_3 - x_2 \right) } </mathtex>
* ...
* <mathtex> P^{n-1}(x)^{(p)} = \sum_{\alpha_1=1}^{n} \frac{ f(x_{\alpha_1}) \sum_{\alpha_{i+1} \neq \alpha_i,\,(i)}^{n,\,(p)} \prod_{\alpha_{p+2} \neq \alpha_{p+1}}^n \left( x - x_{\alpha_{p+2}} \right) }{ \prod_{\alpha_2 \neq \alpha_1}^n \left( x_{\alpha_1} - x_{\alpha_2} \right) } </mathtex>

In particular, if <mathtex>n-1 = p</mathtex> we have,
* <mathtex> P^{p}(x)^{(p)} = \sum_{i=1}^{n} f(x_{i}) \frac{ p }{ \prod_{j \neq i}^n \left( x_{i} - x_{j} \right) } </mathtex>

===[[Compound sum]]===
* <mathtex>\sum^{(p)} = \underbrace{ \sum \circ \sum \circ \ldots \circ \sum }_{p-\text{times}}</mathtex>,
* <mathtex> \sum^{(0)} = id </mathtex>,
* <mathtex> \sum^{n,\,(p)}_{\alpha_{i+1}=1,\,(i)} = \underbrace{ \sum^{n}_{\alpha_2=1} \circ \sum^{n}_{\alpha_3=1} \circ \ldots \circ \sum^{n}_{\alpha_{p+1}=1} }_{p-\text{times}}</mathtex>,

==External references==
*[http://en.wikipedia.org/wiki/Polynomial_interpolation Polynomial interpolation article in wikipedia]

[[Category:Science]]

Compound sum

2008-06-26T21:29:36Z

192.168.20.177:

* <mathtex>\sum^{(p)} = \underbrace{ \sum \circ \sum \circ \ldots \circ \sum }_{p-\text{times}}</mathtex>,
* <mathtex> \sum^{(0)} = id </mathtex>,
* <mathtex> \sum^{n,\,(p)}_{\alpha_{i+1}=1,\,(i)} = \underbrace{ \sum^{n}_{\alpha_2=1} \circ \sum^{n}_{\alpha_3=1} \circ \ldots \circ \sum^{n}_{\alpha_{p+1}=1} }_{p-\text{times}}</mathtex>,

[[Category:Science]]
[[Category:Maths]]

Module LagrangianGlobal

2008-06-25T10:11:03Z

192.168.20.177: /* Overview */

== Overview ==
The LagrangianGlobal module is a module very similar to the [[Module Lagrangian|Lagrangian module]]. The input data file keywords are exactly the same. The modules give the same lagrangian result if the user only runs one model (no nesting).
In the case of the first module when are run several nesting levels. The user only define one lagrangian input data file in the data file of the first nesting level (first model in the tree.dat). Each lagrangian tracer will use the hydrodynamic field with the higher priority depending on the tracer position. By default the priority is define inverting the tree.dat order.
The user can specify the oder using a block define in the lagrangian input file where the user can define the model priority:

<BeginModelPriority>
Model name x
Model name y
<EndModelPriority>

The first model are the one with the higher priority.

If the mohid user wants to activate this module it needs to predefined a preprocessor symbol called _LAGRANGIAN_GLOBAL_ in the compilation phase of the mohid.

== Relative position of tracer in a generic cell ==

A fundamental in the "MOHID system" lagrangian approach is to know the relative position of the tracer in the hydrodynamic cell to speed up the interpolation procedure. This is quite easy for square cells however this not the case for cells of curvilinear grids . In this case was develop a subroutine that is able to compute the generic position of a tracer in a generic cell (see subroutine RelativePosition4VertPolygon in module functions). The algorithm used is described below.

[[Image:FromGenericToSquare.jpg|850px|thumb|center|'''Relative position of tracer in a generic cell''']]

<math> y_1 = a_1 + b_1 x_1 \wedge a_1 = {{x_d y_c - x_c y_d } \over {x_d - x_c }} \wedge b_1 = {{y_d - y{}_c} \over {x_d - x_c }} </math>

<math> y_2 = a_2 + b_2 x_2 \wedge a_2 = {{x_b y_a - x_a y_b } \over {x_b - x_a }} \wedge b_2 = {{y_b - y{}_a} \over {x_b - x_a }} </math>

<math> y_3 = a_3 + b_3 x_3 \wedge a_3 = {{x_a y_c - x_c y_a } \over {x_a - x_c }} \wedge b_3 = {{x_a - x_c } \over {y_a - y{}_c}} </math>

<math> y_4 = a_4 + b_4 x_4 \wedge a_4 = {{x_b y_d - x_d y_b } \over {x_b - x_d }} \wedge b_4 = {{x_b - x_d } \over {y_b - y{}_d}} </math>

<math> y_g = {{a_3 - a_4 } \over {b_4 - b_3 }} \wedge x_g = a_3 + b_3 y_g </math>

if (b1==b2) then
<math> tg\alpha = b_2</math>
else
<math> x_f = {{a_1 - a_2 } \over {b_2 - b_1 }} \wedge y_f = a_1 + b_1 x_f </math>
<math> tg\alpha = {{y_e - y_f } \over {x_e - x_f }} </math>
endif

<math> y_h = {{y_e + \left( {a_3 - x_e } \right)Tg\alpha } \over {1 - b_3 Tg\alpha }} \wedge x_h = a_3 + b_3 y_h </math>

if (b3==b4) then
<math> tg\beta = b_3 </math>
else
<math> x_g = {{a_3 - a_4 } \over {b_4 - b_3 }} \wedge y_g = a_3 + b_3 x_g </math>
<math> tg\beta = {{y_e - y_g } \over {x_e - x_g }} </math>
endif

<math> y_i = {{y_e + \left( {a_1 - x_e } \right)Tg\beta } \over {1 - b_1 Tg\beta }} \wedge x_i = a_1 + b_1 y_i </math>

<math> seg\_ac = \sqrt {\left( {x_a - x_c } \right)^2 + \left( {y_a - y_c } \right)^2 } </math>

<math> seg\_dc = \sqrt {\left( {x_d - x_c } \right)^2 + \left( {y_d - y_c } \right)^2 } </math>

<math> seg\_ic = \sqrt {\left( {x_i - x_c } \right)^2 + \left( {y_i - y_c } \right)^2 } </math>

<math> seg\_hc = \sqrt {\left( {x_h - x_c } \right)^2 + \left( {y_h - y_c } \right)^2 } </math>

<math> x_e^' = {{Seg\_ic} \over {Seg\_dc}} </math>

<math> y_e^' = {{Seg\_hc} \over {Seg\_ac}} </math>

[[Category:Modules]]
[[Category:MOHID Water]]