AutoChem is

NASA The National Aeronautics and Space Administration (NASA ) is an independent agency of the US federal government responsible for the civil space program, aeronautics research, and space research. NASA was established in 1958, succeedi ...

release software that constitutes an automatic computer code generator and documenter for chemically reactive systems written by

David Lary David J. Lary (born 7 December 1965) is a British-American atmospheric scientist interested in applying computational and information systems to facilitate discovery and decision support in Earth system science. His main contributions have been t ...

between 1993 and the present. It was designed primarily for modeling

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 approach of research and draws on environmental chemistry, physics, mete ...

, and in particular, for chemical

data assimilation Data assimilation is a mathematical discipline that seeks to optimally combine theory (usually in the form of a numerical model) with observations. There may be a number of different goals sought – for example, to determine the optimal state es ...

. The user selects a set of chemical species. AutoChem then searches

chemical reaction A chemical reaction is a process that leads to the chemical transformation of one set of chemical substances to another. Classically, chemical reactions encompass changes that only involve the positions of electrons in the forming and break ...

databases for these species and automatically constructs the

ordinary differential equations In mathematics, an ordinary differential equation (ODE) is a differential equation whose unknown(s) consists of one (or more) function(s) of one variable and involves the derivatives of those functions. The term ''ordinary'' is used in contras ...

(ODE) that describe the chemical system. AutoChem symbolically differentiates the time derivatives to give the

Jacobian matrix In vector calculus, the Jacobian matrix (, ) of a vector-valued function of several variables is the matrix of all its first-order partial derivatives. When this matrix is square, that is, when the function takes the same number of variables ...

, and symbolically differentiates the Jacobian matrix to give the

Hessian matrix In mathematics, the Hessian matrix or Hessian is a square matrix of second-order partial derivatives of a scalar-valued function, or scalar field. It describes the local curvature of a function of many variables. The Hessian matrix was developed ...

and the adjoint. The Jacobian matrix is required by many

algorithms In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing ...

that solve the

numerically, particular when the ODEs are stiff. The Hessian matrix and the adjoint are required for four-dimensional variational data assimilation (4D-Var). AutoChem documents the whole process in a set of

LaTeX Latex is an emulsion (stable dispersion) of polymer microparticles in water. Latexes are found in nature, but synthetic latexes are common as well. In nature, latex is found as a milky fluid found in 10% of all flowering plants (angiosper ...

and

PDF Portable Document Format (PDF), standardized as ISO 32000, is a file format developed by Adobe in 1992 to present documents, including text formatting and images, in a manner independent of application software, hardware, and operating systems. ...

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. A huge observational

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spa ...

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 Probability distribution function may refer to: * Probability distribution * Cumulative distribution function * Probability mass function In probability and statistics, a probability mass function is a function that gives the probability that a di ...

s. Such an analysis is available on line at PDFCentral which was designed for the validation of observations from the NASA Aura satellite.

References

Computational chemistry software Chemical kinetics Environmental chemistry {{science-software-stub

See also

References