The Code

The most widely used geochemical modeling programs consist of a computer code plus a related file of data called a database. The database contains thermodynamic and kinetic parameters. The code uses the thermodynamic and kinetic parameters in the database and concentrations or other constraints as input, and produces results that describe a geochemical model for a particular chemical system. 

In this chapter we shall limit our discussion of the codes to speciation-solubility and reaction path modeling codes. Coupled reactive mass transport codes are much more mathematically and computationally complex. The readers can find recent discussions in Lichtner (1996) and Steefel and MacQuarrie (1996). 

A computer modeling code or program is a set of computer commands that include algorithms to solve a set of mathematical equations describing chemical equilibria, 

Algorithms The numerical techniques embodied in the computer code Computer code The assembly of numerical techniques, bookkeeping, and control language that represents the model from acceptance of input data and instruction to delivery of output Model The assembly of concepts in the form of mathematical 

The codes published by government agencies (minteqa2, EQ3/6, and phreeqc) have all gone through some, at times lengthy, quality assurance/quality control (QA/QC) procedures, and are verified against other codes or hand calculations for their mathematical functionality. In other words, they perform the calculations they are supposed to do 

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NMD(1,J) cols 1-6 six-character identification code for component one this must match the code read in with the pure-component data. 

However, such a situation implies a risk. Industry tends to cut costs on commodities such as NDT, especially when they are needed because the code says so. And therefore NDT prices are under pressure, and competition is heavy. 

This presentation will highlight some NDT applications whereby NDT can be transformed from a "necessary evil" into a situation that is "of beneficial value" to the user. From an activity that has to be done because it is required by the code, to a solution to a problem that can improve safety, enhance quality and save money. 

In an ambitious study, the AIMS method was used to calculate the absorption and resonance Raman spectra of ethylene [221]. In this, sets starting with 10 functions were calculated. To cope with the huge resources required for these calculations the code was parallelized. The spectra, obtained from the autocorrelation function, compare well with the experimental ones. It was also found that the non-adiabatic processes described above do not influence the spectra, as their profiles are formed in the time before the packet reaches the intersection, that is, the observed dynamic is dominated by the torsional motion. Calculations using the Condon approximation were also compared to calculations implicitly including the transition dipole, and little difference was seen. 

After the assembling of the stochastic matrix Pd we have to solve the associated non-selfadjoint eigenvalue problem. Our present numerical results have been computed using the code speig by Radke AND S0RENSEN in Matlab,... 

The first line notations were conceived before the advent of computers. Soon it was realized that the compactness of such a notation was well suited to be handled by computers, because file storage space was expensive at that time. The heyday of line notations were between I960 and 1970, A chemist, trained in this line notation. could enter the code of large molecules faster than with a structure-editing program,... 

The ROSDAL syntax is characterized by a simple coding of a chemical structure using alphanumeric symbols which can easily be learned by a chemist [14]. In the linear structure representation, each atom of the structure is arbitrarily assigned a unique number, except for the hydrogen atoms. Carbon atoms are shown in the notation only by digits. The other types of atoms carry, in addition, their atomic symbol. In order to describe the bonds between atoms, bond symbols are inserted between the atom numbers. Branches are marked and separated from the other parts of the code by commas [15, 16] (Figure 2-9). The ROSDAL linear notation is rmambiguous but not unique. 

ROSDAL is used in the Beilstein-DIALOG system [17] as a data exchange format. The code can represent not only full structures and substructures but also some generic structures. 

A special extension of SMILES is USMILES (sometimes described as Broad SMILES) [23-25]. This Unique SMILES of Daylight is a canonical representation of a structure. This means that the coding is independent of the internal atomic numbering and results always in the same canonical, unambiguous, and unique description of the compound, granted by an algorithm (see Section 2.5.2). 

In contrast to canonical linear notations and connection tables (see Sections 2.3 and 2.4), fragment codes arc ambiguous. Several different structures could all possess an identical fragment code, because the code docs not describe how the fragments arc interconnected. Moreover, it is not always evident to the user whether all possible fi aginents of the stmetures ai e at all accessible. Thus, the fragments more or less characterise a class of molecules this is also important in generic structures that arise in chemical patents (sec Section 2.7.1)... 

Hash codes of molecules which are already pre-computed are suitable for use in fiill structure searches in database applications. The compression of the code of a chemical structure into only one number also makes it possible to compute in advance the transformation results for a whole catalog. The files can be stored and kept complete in the core memory during execution of the program, so that a search can be accomplished within seconds. 

The data analysis module of ELECTRAS is twofold. One part was designed for general statistical data analysis of numerical data. The second part offers a module For analyzing chemical data. The difference between the two modules is that the module for mere statistics applies the stati.stical methods or rieural networks directly to the input data while the module for chemical data analysis also contains methods for the calculation ol descriptors for chemical structures (cl. Chapter 8) Descriptors, and thus structure codes, are calculated for the input structures and then the statistical methods and neural networks can be applied to the codes. 

Note MM-i- is derived from the public domain code developed by Dr. Norm an Allinger, referred to as M.M2( 1977), and distributed by the Quantum Chemistry Program Exchange (QCPE). The code for MM-t is not derived from Dr. Allin ger s present version of code, which IS trademarked MM2 . Specifically. QCMPOlO was used as a starting point Ibr HyperChem MM-t code. The code was extensively modified and extended over several years to include molecular dynamics, switching functuins for cubic stretch terms, periodic boundary conditions, superimposed restraints, a default (additional) parameter scheme, and so on. 

Quantum chemists have devised efficient short-hand notation schemes to denote the basis set aseti in an ab initio calculation, although this does mean that a proliferation of abbrevia-liijii.s and acronyms are introduced. However, the codes are usually quite simple to under-sland. We shall concentrate on the notation used by Pople and co-workers in their Gaussian aerie-, of programs (see also the appendix to this chapter). 

ZINDO is an adaptation of INDO speciflcally for predicting electronic excitations. The proper acronym for ZINDO is INDO/S (spectroscopic INDO), but the ZINDO moniker is more commonly used. ZINDO has been fairly successful in modeling electronic excited states. Some of the codes incorporated in ZINDO include transition-dipole moment computation so that peak intensities as well as wave lengths can be computed. ZINDO generally does poorly for geometry optimization. 

NWChem (we tested Version 3.2.1) is a program for ah initio, band-structure, molecular mechanics, and molecular dynamics calculations. The DFT band-structure capability is still under development and was not included in the Linux version tested. NWChem is unique in that it was designed from scratch for efficient parallel execution. The user agreement is more restrictive than most, apparently because the code is still under active development. At the time of this book s publication, limited support was available for users outside of the EMSL facility. 

NWChem uses ASCII input and output files. The input format allows geometry to be input as Cartesian coordinates or a Z-matrix. If symmetry is specified, only the Cartesian coordinates of the symmetry-unique atoms are included. Some sections of the code require additional input files. 

The molecular mechanics force helds available are AMBER95 and CFIARMM. The molecular mechanics and dynamics portion of the code is capable of performing very sophisticated calculations. This is implemented through a large number of data hies used to hold different types of information along with keywords to create, use, process, and preprocess this information. This results in having a very hexible program, but it makes the input for simple calculations unnecessarily complex. QM/MM minimization and dynamics calculations are also possible. 

MOFPRO (we tested Version 98.1) is an ah initio program designed for performing complex calculations. This program is often used for calculations that present technical difficulties or are very sensitive to electron correlation. A few portions of the code have been parallelized. 

Gaussian users will find that Q-Chem feels familiar. The ASCII input format is a bit more wordy than Gaussian it is more similar to GAMESS input. The output is very similar to Gaussian output, but a bit cleaner. The code can easily be used with a job-queueing system. 

Modify Figure 28 12 so that it corresponds to translation of an mRNA in which the sequence of the first six bases of the coding sequence are AUGUCU... 

The HyperChem MMh- code and program also differ from MM2(1977) by having parameters in text files separate from the code. These parameter files are available for your modification and additions. The parameters distributed with HyperChem include the public domain values, generally referred to as the MM2(1991) parameter set, that Dr. Allinger contributed to HyperCube, Inc. Parameters not obtained from Dr. Allinger are appropriately labeled in the distributed parameter files. 

Table 14.5 lists the uncoded factor levels, coded factor levels, and responses for a 2 factorial design. Determine the coded and uncoded empirical model for the response surface based on equation 14.10. 

To check the result we substitute the coded factor levels for the first run into the coded empirical model, giving... 

To transform the coded empirical model into its uncoded form, it is necessary to replace A, B, and C with the following relationships... 

Determine the coded and uncoded equation for the response surface. 

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