Difference between revisions of "Tools portal"

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Landlab is an open-source Python library of code that enables users to easily build unique earth surface processes models to address specific hypotheses. The Landlab library contains gridding engines for building regular and irregular grids, process components that act on grid variables, tools for storing and sharing data among the grid and components, and plotting and analysis tools. Process components represent individual processes occurring at the earth’s surface (e.g. growth and death of vegetation, surface water infiltration, linear diffusion of sediment), or drivers of these processes (e.g. rainfall, solar radiation). Users can build models by combining existing process components, or build new components if a required process component does not exist. Landlab was developed by members of the CSDMS community with support from CSDMS and the National Science Foundation (two ACI - SI2 grants).  
[http://landlab.github.io LANDLAB] is an open-source Python library of code that enables users to easily build unique earth surface processes models to address specific hypotheses. The Landlab library contains gridding engines for building regular and irregular grids, process components that act on grid variables, tools for storing and sharing data among the grid and components, and plotting and analysis tools. Process components represent individual processes occurring at the earth’s surface (e.g. growth and death of vegetation, surface water infiltration, linear diffusion of sediment), or drivers of these processes (e.g. rainfall, solar radiation). Users can build models by combining existing process components, or build new components if a required process component does not exist. Landlab was developed by members of the CSDMS community with support from CSDMS and the National Science Foundation (two ACI - SI2 grants).  


'''Why build another modeling tool?'''<br>Landlab has the rare distinction of being built to make modeling accessible to a wide variety of earth scientists, including those who do not traditionally use computational models. In contrast, most other models are designed to answer a specific hypothesis posed by the developers.  
'''Why build another modeling tool?'''<br>Landlab has the rare distinction of being built to make modeling accessible to a wide variety of earth scientists, including those who do not traditionally use computational models. In contrast, most other models are designed to answer a specific hypothesis posed by the developers.  

Revision as of 14:03, 13 April 2018

Modeling Tools

The CSDMS software engineers create tools to help CSDMS members couple and run models.

BMI Builder

The Basic Model Interface

The BMI Builder helps developers build a Basic Model Interface for their model by generating template source code which is then customized by the user for their particular model. Users provide some basic metadata for their model (such as names of input and output items, units, etc.) to the bmi builder which then creates creates BMI implementation files in their language of choice. The user then go through these file of files and implements the labeled sections.

Links

  • Source code on GitHub
  • Documentation on how to use the BMI Builder is provided on GitHub in the read.me file

BMI Tester

The BMI Tester is a Python package that provides command-line utilities for testing Python classes that implement the Basic Model Interface (BMI). BMI Tester also provides a Python interface to the tester that allows users to run tests programmatically. The package is easily extendable so that new tests can be added to the suite.

Links

Standard Names registry

The Standard Names registry is a Python library for working with CSDMS Standard Names.

The CSDMS Standard Names provide a comprehensive set of naming rules and patterns that are not specific to any particular modeling domain. They were also designed to have many other nice features such as parsability and natural alphabetical grouping. CSDMS Standard Names always consist of an object part and a quantity/attribute part and the quantity part may also have an operation prefix which can consist of multiple operations.

standard_names is a Python package to define, query, operate, and manipulate CSDMS Standard Names. It is distributed with a comprehensive list of the currently defined Standard Names.

The standard_names package consists of two basic classes:

  • StandardName: a single name
  • NamesRegistry: a collection of names.

The standard_names package has a complete set of unit tests that are continually tested on Mac, Linux, and Windows. It is distributed both as source code and as Anaconda packages from Anaconda Cloud.

Links

WMT

The CSDMS Web Modeling Tool

The CSDMS Web Modeling Tool, WMT, is a web application that allows users on a desktop, laptop or tablet computer to build and run standalone or coupled Earth surface dynamics models on a supercomputer.

With WMT, users can:

  • Design a model from a set of CSDMS components
  • Edit model parameters
  • Save models to a web-accessible server
  • Share saved models with the community
  • Submit model runs to an HPC system
  • Download simulation results

The following components are currently available in WMT.

To see how you can use WMT to configure and run a standalone or a coupled model on the web, check out the WMT tutorial, or jump right into using WMT at https://csdms.colorado.edu/wmt.

For more information on WMT, including links to its documentation and its source code repositories, please see the CSDMS Web Modeling Tool wiki page.

PyMT

Pymt-logo-cropped.png

PyMT is an Open Source Python package, developed by the Community Surface Dynamics Modeling System, that provides the necessary tools used for the coupling of models that expose the Basic Modeling Interface (BMI). It contains:

  • Tools necessary for coupling models of disparate time and space scales (including grid mappers)
  • Time-steppers that coordinate the sequencing of coupled models
  • Exchange of data between BMI-enabled models
  • Wrappers that automatically load BMI-enabled models into the PyMT framework
  • Utilities that support open-source interfaces (UGRID, SGRID, CSDMS Standard Names, etc.)
  • A collection of community-submitted models, written in a variety of programming languages, from a variety of process domains - but all usable from within the Python programming language
  • A plug-in framework for adding additional BMI-enabled models to the framework

Dakotathon

Dakotathon.jpg

Dakota is a software toolkit developed at Sandia National Laboratories that provides an interface between models and a library of analysis methods, including support for sensitivity analysis, uncertainty quantification, optimization, and calibration techniques. Dakota is a powerful tool, but its learning curve is steep: the user not only must understand the structure and syntax of the Dakota input file, but also must develop intermediate code that allows Dakota to set up and run a model, read outputs from the model, and calculate a response statistic from the outputs.

The CSDMS Dakota Interface, or Dakotathon, is a Python package that wraps and extends Dakota’s file-based user interface. It simplifies the process of configuring and running a Dakota experiment, and it allows a Dakota experiment to be scripted. Dakotathon creates the Dakota input file and provides a generic analysis driver. Any model componentized in the CSDMS modeling framework automatically works with Dakotathon. Dakotathon has a plugin architecture, so models not wrapped into the CSDMS modeling framework can be accessed by Dakotathon by programmatically extending a template; an example is provided in the Dakotathon distribution.

For more information on Dakotathon, including links to its documentation and its source code repository, please see the Dakotathon wiki page.

Landlab

Landlab logo picture.jpg

LANDLAB is an open-source Python library of code that enables users to easily build unique earth surface processes models to address specific hypotheses. The Landlab library contains gridding engines for building regular and irregular grids, process components that act on grid variables, tools for storing and sharing data among the grid and components, and plotting and analysis tools. Process components represent individual processes occurring at the earth’s surface (e.g. growth and death of vegetation, surface water infiltration, linear diffusion of sediment), or drivers of these processes (e.g. rainfall, solar radiation). Users can build models by combining existing process components, or build new components if a required process component does not exist. Landlab was developed by members of the CSDMS community with support from CSDMS and the National Science Foundation (two ACI - SI2 grants).

Why build another modeling tool?
Landlab has the rare distinction of being built to make modeling accessible to a wide variety of earth scientists, including those who do not traditionally use computational models. In contrast, most other models are designed to answer a specific hypothesis posed by the developers.

What does this mean for new users?

  • Landlab is extensively documented.
  • Users can contact developers with issues.
  • There are tutorials to teach users how to use Landlab.
  • There are classroom tutorials to teach students about different surface processes.
  • Many Landlab tutorials are accessible through Hydroshare, an online collaborative environment for sharing data and models, which allows users to test-out Landlab without installing it locally.
  • Landlab has integrated testing to ensure that new code contributions will not break existing code.
  • There is documentation to make contributing code a bit easier.

Landlab Components and Models
Numerous people have contributed components and models to landlab. Of these, 52 are described in the CSDMS repository and are listed below.

ProgramDescriptionDeveloperDownloadPyMT
ChannelProfiler The ChannelProfiler extracts and plots channel networks from a landlab grid. Barnhart, Katy
redirect download
ChiFinder Calculate Chi Indices Hobley, Daniel
redirect download
DepressionFinderAndRouter Find depressions on a topographic surface. Hobley, Dan
redirect download
DepthDependentDiffuser
A.k.a. Landlab Depth Dependent Linear Diffuser
Soil depth-dependent linear hillslope diffuser Glade, Rachel
redirect download
DepthDependentTaylorDiffuser This component implements a depth-dependent Taylor series diffusion rule, combining concepts of Ganti et al. (2012) and Johnstone and Hilley (2014). Glade, Rachel
redirect download
DetachmentLtdErosion Simulate detachment limited sediment transport. Adams, Jordan
redirect download
Drainage Density
A.k.a. Landlab Drainage Density tool
Component for calculating drainage density in Landlab given a channel network Shobe, Charles
redirect download
ErosionDeposition
A.k.a. Landlab ErosionDeposition component
Landlab component for fluvial erosion/deposition. Shobe, Charles
redirect download
ExponentialWeatherer Exponential soil production function in the style of Ahnert (1976) Glade, Rachel
redirect download
FastscapeEroder Compute fluvial erosion using stream power theory (“fastscape” algorithm) Hobley, Daniel
redirect download
FireGenerator This component generates a random fire event or fire time series from the Weibull statistical distribution. Adams, Jordan
redirect download
Flexure Deform the lithosphere with 1D or 2D flexure. Hutton, Eric
redirect download
FlowAccumulator Component to accumulate flow and calculate drainage area. Barnhart, Katy
redirect download
FlowDirectorD8 Single-path (steepest direction) flow direction with diagonals on rasters. Barnhart, Katy
redirect download
FlowDirectorDinf Flow direction on a raster grid by the D infinity method. Barnhart, Katy
redirect download
FlowDirectorMFD Multiple-path flow direction with or without out diagonals. Barnhart, Katy
redirect download
FlowDirectorSteepest Single-path (steepest direction) flow direction without diagonals. Barnhart, Katy
redirect download
FractureGridGenerator Create a 2D grid with randomly generated fractures. Tucker, Greg
redirect download
GrainHill
A.k.a. Grain Hill
Cellular automaton model of hillslope evolution Tucker, Gregory
redirect download
GroundwaterDupuitPercolator The GroundwaterDupuitPercolator solves the Boussinesq equation for flow in an unconfined aquifer over an impermeable aquifer base and calculates groundwater return flow to the surface. Litwin, David
redirect download
HackCalculator Calculate Hack parameters. Barnhart, Katy
redirect download
LakeMapperBarnes Temporarily fills depressions and reroutes flow across them Hobley, Daniel
redirect download
Landlab Python software framework for writing, assembling, and running 2D numerical models Tucker, Greg
redirect download
Landslides Landlab component that simulates landslide probability of failure as well as mean relative wetness and probability of saturation. Strauch, Ronda
redirect download
LateralEroder Laterally erode neighbor node through fluvial erosion. Langston, Abigail
redirect download
LinearDiffuser Landlab component that models soil creep as a linear diffusion process Tucker, Greg
redirect download
Lithology Create a Lithology object with different properties Barnhart, Katy
redirect download
LossyFlowAccumulator Component to calculate drainage area and accumulate flow, while permitting dynamic loss or gain of flow downstream. Hobley, Dan
redirect download
NormalFault NormalFault implements relative rock motion due to a normal fault. Barnhart, Katy
redirect download
OverlandFlow
A.k.a. Landlab OverlandFlow component
Component simulating overland flow using a 2-D numerical approximation of the shallow-water equations following the de Almeida et al., 2012 algorithm for storage-cell inundation modeling. Adams, Jordan
redirect download
OverlandFlowBates This component simulates overland flow using the 2-D numerical model of shallow-water flow over topography using the Bates et al. (2010) algorithm for storage-cell inundation modeling. Adams, Jordan
redirect download
PerronNLDiffuse Nonlinear diffusion, following Perron (2011). Hobley, Daniel
redirect download
PotentialEvapotranspiration Calculates potential evapotranspiration Nudurupati, Sai
redirect download
PotentialityFlowRouter Multidirectional flow routing using a novel method. Hobley, Daniel
redirect download
PrecipitationDistribution Generate random sequence of precipitation events Adams, Jordan
redirect download
Radiation Compute 1D and 2D total incident shortwave radiation. Nudurupati, Sai
redirect download
SPACE
A.k.a. Landlab Stream Power with Alluvium Conservation and Entrainment component
Landlab component for 2-D calculation of fluvial sediment transport and bedrock erosion Shobe, Charles
redirect download
SedDepEroder Compute fluvial erosion using using “tools and cover” theory Hobley, Daniel
redirect download
SinkFiller Fill sinks in a landscape to the brim, following the Barnes et al. (2014) algorithms. Hobley, Daniel
redirect download
SoilInfiltrationGreenAmpt
A.k.a. The Landlab SoilInfiltrationGreenAmpt component
Landlab component that calculates soil infiltration based on the Green-Ampt solution. Rengers, Francis
redirect download
SoilMoisture Compute the decay of soil moisture saturation at storm-interstorm time period Nudurupati, Sai
redirect download
SpatialPrecipitationDistribution Generate random sequence of spatially-resolved precipitation events Hobley, Daniel
redirect download
SpeciesEvolver Evolve life in a landscape. Lyons, Nathan
redirect download
SteepnessFinder Calculate steepness and concavity indices from gridded topography Hobley, Daniel
redirect download
StreamPowerSmoothThresholdEroder Compute fluvial erosion using stream power theory with a numerically smoothed threshold Tucker, Greg
redirect download
TaylorNonLinearDiffuser Model non-linear soil creep after Ganti et al. (2012) Glade, Rachel
redirect download
Terrainbento
A.k.a. terrainbento
A Python package for multi-model analysis in long-term drainage basin evolution Barnhart, Katy
redirect download
TransportLengthHillslopeDiffuser Transport length hillslope diffusion. Mouchene, Margaux
redirect download
VegCA Landlab component that simulates inter-species plant competition using a 2D cellular automata model. Nudurupati, Sai
redirect download
Vegetation Model plant dynamics using multiple representative plant species Nudurupati, Sai
redirect download
ZoneController Controls zones and populates them with taxa. Lyons, Nathan
redirect download
ZoneTaxon A zone-based taxon Lyons, Nathan
redirect download