Autochem
Encyclopedia
AutoChem is NASA
release software that constitutes an automatic computer code generator and documenter for chemically reactive systems http://www.nasatech.com/Briefs/Nov05/GSC_14862_1.html written by David Lary
between 1993 and the present. It was designed primarily for modeling atmospheric chemistry
, and in particular, for chemical data assimilation
.
The user selects a set of chemical species. AutoChem then searches chemical reaction
databases for these species and automatically constructs the ordinary differential equations (ODE) that describe the chemical system. AutoChem symbolically differentiates
the time derivatives to give the Jacobian matrix, and symbolically differentiates
the Jacobian matrix to give the Hessian matrix
and the adjoint
. The Jacobian matrix is required by many algorithms that solve the ordinary differential equations numerically, particular when the ODEs are stiff. The Hessian matrix
and the adjoint
are required for 4dimensional variational data assimilation (4D-Var). AutoChem documents the whole process in a set of LaTeX
and PDF files.
The reactions involving the user specified constituents are extracted by the first AutoChem preprocessor program called Pick. This subset of reactions is then used by the second AutoChem preprocessor program RoC (rate of change) to generate the time derivatives, Jacobian, and Hessian. Once the two preprocessor programs have run to completion all the Fortran 90 code has been generated that is necessary for modeling and assimilating the kinetic processes.
An online AutoChem manual is available. In addition, a huge observational database
of many different atmospheric constituents from a host of platforms are available from the AutoChem site.
AutoChem has been used to perform long term chemical data assimilation of atmospheric chemistry
. This assimilation was automatically documented by the AutoChem software and is available on line at CDACentral. Data quality is always an issue for chemical data assimilation, in particular the presence of biases. To identify and understand the biases it is useful to compare observations using probability distribution function
s. Such an analysis is available on line at PDFCentral which was designed for the validation of observations from the NASA Aura satellite
.
NASA
The National Aeronautics and Space Administration is the agency of the United States government that is responsible for the nation's civilian space program and for aeronautics and aerospace research...
release software that constitutes an automatic computer code generator and documenter for chemically reactive systems http://www.nasatech.com/Briefs/Nov05/GSC_14862_1.html written by David Lary
David Lary
David Lary is an atmospheric scientist interested in applying computational and information systems to facilitate discovery and decision support in Earth System Science...
between 1993 and the present. It was designed primarily for modeling atmospheric chemistry
Atmospheric chemistry
Atmospheric chemistry is a branch of atmospheric science in which the chemistry of the Earth's atmosphere and that of other planets is studied. It is a multidisciplinary field of research and draws on environmental chemistry, physics, meteorology, computer modeling, oceanography, geology and...
, and in particular, for chemical data assimilation
Data assimilation
Applications of data assimilation arise in many fields of geosciences, perhaps most importantly in weather forecasting and hydrology. Data assimilation proceeds by analysis cycles...
.
The user selects a set of chemical species. AutoChem then searches chemical reaction
Chemical reaction
A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. Chemical reactions can be either spontaneous, requiring no input of energy, or non-spontaneous, typically following the input of some type of energy, such as heat, light or electricity...
databases for these species and automatically constructs the ordinary differential equations (ODE) that describe the chemical system. AutoChem symbolically differentiates
Derivative
In calculus, a branch of mathematics, the derivative is a measure of how a function changes as its input changes. Loosely speaking, a derivative can be thought of as how much one quantity is changing in response to changes in some other quantity; for example, the derivative of the position of a...
the time derivatives to give the Jacobian matrix, and symbolically differentiates
Derivative
In calculus, a branch of mathematics, the derivative is a measure of how a function changes as its input changes. Loosely speaking, a derivative can be thought of as how much one quantity is changing in response to changes in some other quantity; for example, the derivative of the position of a...
the Jacobian matrix to give the Hessian matrix
Hessian matrix
In mathematics, the Hessian matrix is the square matrix of second-order partial derivatives of a function; that is, it describes the local curvature of a function of many variables. The Hessian matrix was developed in the 19th century by the German mathematician Ludwig Otto Hesse and later named...
and the adjoint
Adjoint
In mathematics, the term adjoint applies in several situations. Several of these share a similar formalism: if A is adjoint to B, then there is typically some formula of the type = .Specifically, adjoint may mean:...
. The Jacobian matrix is required by many algorithms that solve the ordinary differential equations numerically, particular when the ODEs are stiff. The Hessian matrix
Hessian matrix
In mathematics, the Hessian matrix is the square matrix of second-order partial derivatives of a function; that is, it describes the local curvature of a function of many variables. The Hessian matrix was developed in the 19th century by the German mathematician Ludwig Otto Hesse and later named...
and the adjoint
Adjoint
In mathematics, the term adjoint applies in several situations. Several of these share a similar formalism: if A is adjoint to B, then there is typically some formula of the type = .Specifically, adjoint may mean:...
are required for 4dimensional variational data assimilation (4D-Var). AutoChem documents the whole process in a set of LaTeX
LaTeX
LaTeX is a document markup language and document preparation system for the TeX typesetting program. Within the typesetting system, its name is styled as . The term LaTeX refers only to the language in which documents are written, not to the editor used to write those documents. In order to...
and PDF files.
The reactions involving the user specified constituents are extracted by the first AutoChem preprocessor program called Pick. This subset of reactions is then used by the second AutoChem preprocessor program RoC (rate of change) to generate the time derivatives, Jacobian, and Hessian. Once the two preprocessor programs have run to completion all the Fortran 90 code has been generated that is necessary for modeling and assimilating the kinetic processes.
An online AutoChem manual is available. In addition, a huge observational database
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
of many different atmospheric constituents from a host of platforms are available from the AutoChem site.
AutoChem has been used to perform long term chemical data assimilation of atmospheric chemistry
Atmospheric chemistry
Atmospheric chemistry is a branch of atmospheric science in which the chemistry of the Earth's atmosphere and that of other planets is studied. It is a multidisciplinary field of research and draws on environmental chemistry, physics, meteorology, computer modeling, oceanography, geology and...
. This assimilation was automatically documented by the AutoChem software and is available on line at CDACentral. Data quality is always an issue for chemical data assimilation, in particular the presence of biases. To identify and understand the biases it is useful to compare observations using probability distribution function
Probability distribution function
Depending upon which text is consulted, a probability distribution function is any of:* a probability distribution function,* a cumulative distribution function,* a probability mass function, or* a probability density function....
s. Such an analysis is available on line at PDFCentral which was designed for the validation of observations from the NASA Aura satellite
Aura (satellite)
Aura is a multi-national NASA scientific research satellite in orbit around the Earth, studying the Earth's ozone layer, air quality and climate. It is the third major component of the Earth Observing System following on Terra and Aqua...
.