AutoChem is

NASA The National Aeronautics and Space Administration (NASA ) is an independent agencies of the United States government, independent agency of the federal government of the United States, US federal government responsible for the United States ...

release software that constitutes an automatic computer code generator and documenter for chemically reactive systems written by David Lary between 1993 and the present. It was designed primarily for modeling

atmospheric chemistry Atmospheric chemistry is a branch of atmospheric science that studies the chemistry of the Earth's atmosphere and that of other planets. This multidisciplinary approach of research draws on environmental chemistry, physics, meteorology, comput ...

, and in particular, for chemical

data assimilation Data assimilation refers to a large group of methods that update information from numerical computer models with information from observations. Data assimilation is used to update model states, model trajectories over time, model parameters, and ...

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

chemical reaction A chemical reaction is a process that leads to the chemistry, chemical transformation of one set of chemical substances to another. When chemical reactions occur, the atoms are rearranged and the reaction is accompanied by an Gibbs free energy, ...

databases for these species and automatically constructs the

ordinary differential equations In mathematics, an ordinary differential equation (ODE) is a differential equation (DE) dependent on only a single independent variable. As with any other DE, its unknown(s) consists of one (or more) function(s) and involves the derivatives ...

(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. If this matrix is square, that is, if the number of variables equals the number of component ...

, and symbolically differentiates the Jacobian matrix to give the

Hessian matrix In mathematics, the Hessian matrix, Hessian or (less commonly) Hesse matrix is a square matrix of second-order partial derivatives of a scalar-valued Function (mathematics), function, or scalar field. It describes the local curvature of a functio ...

and the adjoint. The Jacobian matrix is required by many

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

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. Latices are found in nature, but synthetic latices are common as well. In nature, latex is found as a wikt:milky, milky fluid, which is present in 10% of all floweri ...

and

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

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 or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...

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 functions. 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 {{chem-software-stub

See also

References