INFOREX-3.0: A database on experimental studies of phase equilibria in igneous rocks and synthetic systems: II. Data description and petrological applications

The purpose of the paper is to provide details of the application of the INFOREX-3.0 database, a package designed to store, retrieve, and process phase equilibria information. This most recent release of the system accesses data of 162 experimental studies, conducted from 1962 to 1994, including a total of 6174 experiments with 5188 addressed to natural igneous rocks and 986 runs carried out in synthetic systems, mostly CMAS. The total database was divided into 3893 “dry” conditions experiments, and 2281 runs performed in the presence of H₂O and/or CO₂: 1618 of the “wet” runs represented are water saturated. The number of 1 atm experiments (3750) is greater than the number of high-pressure runs (2474). The INFOREX database contains 8311 coexisting phase compositions: 3197 for glasses, 1247—olivine, 1429—pyroxenes, 501—spinels, 842—plagioclase. One block of the INFOREX information includes 298 liquid compositions where the Fe³⁺/Fe²⁺ ratio was determined. Data for sulfur and water solubility experiments also have been systematized. The INFOREX data management system allows users to find and print out data on a specific set of mineral-melt or two mineral equilibrium experiments requested for a given range of temperatures, pressures, oxygen fugacities, and compositions in a matter of a few seconds. In addition, one can use subsets of the data to develop mineral-melt geothermometers for equilibria including olivine, plagioclase, pyroxenes, and spinels for any specific system type. Two examples illustrate the use of INFOREX for testing empirical equations proposed for the calculation of water solubility and Fe³⁺/Fe²⁺ ratio in basic to acid melts.     

Qmol: a program for molecular visualization on Windows-based PCs

With the advent of powerful, inexpensive graphics hardware, a variety of molecular modelling tools are now available for personal computers (PCs). While a host of high-quality, free visualization programs exist for Unix-like operating systems, there are relatively few available for Microsoft Windows. Most programs that do run under Windows are designed to interactively visualize experimental data and cannot read binary trajectory data generated by molecular simulations. In addition, many of these programs do not accept command line arguments, limiting their ability to serve as a “helper” application to be run by other applications. To fill this gap in functionality, we present Qmol—a program designed for viewing the output of simulations and theoretical calculations of peptides and small molecules.     

PT-system, TX-system, PX-system: Three programs which calculate pressure-temperature-composition phase diagrams

PT-SYSTEM, TX-SYSTEM, and PX-SYSTEM are three FORTRAN 77 programs that calculate complete pressure-temperature (P-T), temperature-composition (T-X_H2O-CO2), and pressure-composition (P-X_H2O-CO2) diagrams. The output of these programs can be plotted for visual representation of phase relations, or inspected from tables. The programs initially generate all possible reactions in the user-specified compositional and PTX space. At the user's option, each point of every reaction is tested for stability with respect to all other phases in the system, and metastable extensions are erased. If a curve is metastable completely, the list of remaining reactions is pruned of those which are metastable entirely within the specified PTX limits of the diagram. Finally, all curves are labeled with stable assemblages.The software is distributed with a recommended thermodynamic database, but a variety of equations of state are provided so that the programs can be used with different data sets. Functions are provided for temperature-dependent disordering, polymorphic transitions, and solid solutions. Run-time options include setting the P, T, X limits of the diagram, the selection of different routines for calculating gas properties, and the specification of fixed phase activities. The user also can specify that only curves stable in the presence of a given phase or assemblage be computed, so that the stability fields of particular phases or assemblages can be identified readily.Copies of the programs (written in ANSI standard FORTRAN 77), the database, and accompanying documentation are available from the senior author.     

FLASK-SG: A program to compute chemical equilibria in metamorphic petrology

Chemical equilibrium calculation program for metamorphic petrology, FLASK-SG, was written for Unix variants (Linux, IRIX, Tru64 UNIX). It is also ported to Windows 95/98. The user specifies a temperature, pressure, and substance amounts (in moles of any chemical formula in C–H–O–Si–Al–Ti–Fe–Mn–Mg–Ca–Na–K system) to this program, then it calculates the stable mineral assemblage, mineral amounts, and gas composition under the given conditions using Gibbs free energy minimization method with the Holland and Powell (1990) data set. Searching algorithm for the stable mineral assemblage is the Metropolis Monte Carlo method. The coding language is C++, and experimental object oriented programming style is adopted to make the main program part as a class library. Model-dependent functions such as fugacity coefficients and activities are implemented as virtual methods of the “systems” class, so they can be easily changed as methods of inherited class from the “systems” class. These characteristics are aimed for a future “simulation kit”.     

Thermodynamic modeling of the Sn–V binary system

The Sn–V binary system was thermodynamically modeled using the CALPHAD approach combined with first-principles calculations. The predicted Gibbs free energy of the end-members in sublattice models of “ V ₃Sn” phase by the first-principles calculations was used to describe the lattice stabilities. A set of thermodynamic parameters for the Sn–V system was obtained using the PanOptimizer program in Pandat software. The calculated phase diagram and thermodynamic properties agree well with the reported experimental data.     

A FORTRAN IV program for the analysis of tectonic strain using deformed elliptical markers

A FORTRAN IV computer program is presented which provides an objective approach to tectonic-strain marker analysis. The algorithms are based on the “Theta-Curve” method and include a test (chi-square, goodness of fit) to check the validity of an initially random marker deformation model. Graphically represented values of confidence versus calculated tectonic-strain estimates, are produced for critical interpretation of results.Orientation data are not dependent on any preconceived reference directions such as cleavage or bedding. The method does assume, in its undeforming procedure, that the median value of the deformed marker-orientations is equivalent to the direction of maximum extension in the finite-strain ellipse.Optional line-printer graphics in separate subroutine form are included for producing the widely accepted diagrams and may be interfaced easily with other strain-analysis programs. A data-conversion program is appended to enable the use of preexisting data sets intended for the STRANE program of Dunnet and Siddans.     

A persistent complex object database language

To support a number of emerging applications we propose a persistent complex object database language which is “value” based. The object space is built through the set and tuple object constructors, with practically no normalization constraints on the nesting levels. The proposed persistent database language can serve both as an interface language to the database management system in itself or as the target language of a conceptual data language. Some of the features of the language include: (i) Notion of “path's” capturing logical references to retrieve and update the persistent database, (ii) a rich set of allowable schema types, including disjuncts, and (iii) a collection of powerful operator constructors for sets.     

BACTID: a microcomputer implementation of a PASCAL program for bacterial identification based on Bayesean probability

A computer program (BACTID) is described which enables the identification of bacteria based on a priori data and Bayesean probability testing. The program is not limited to a specific format, has a short execution time, can be easily applied to a variety of situations, and can be run on almost any microcomputer system operating under either 8-bit CP/M or 16-bit MS-DOS or PC-DOS. Additionally, BACTID is not limited to one type of computer (hardware independent); is not limited by size of the computer's random access memory (RAM independent); can recognize various database matrices (format independent); is able to compensate for missing data; and allows for various methods of data entry. The efficacy of the program was checked against a commercially available test system and a 99.34% agreement was obtained. Also, the execution time for a 46 x 21 data matrix was as little as 3.5 seconds. These results show that microcomputer identification programs not only are viable alternatives to code-book registers, but also offer flexibility which is not found in commercial systems.     

Writing friendly programs in modular form

Friendly software is defined as computer programs which can be run interactively and profitably without incurring fatal errors causing execution termination. We discuss a modular library and a simple program structure providing for input validation, help, status, overview and change commands in a standard FORTRAN environment. As an illustration we show how program WONPSE [Computers Chem.13, 201 (1989)] was easily transformed from a conventional program into a friendly tool for frontier research and student training on N-electron symmetry-eigenfunctions.     

The development of GRAMSKIL: A call grammar program for learners of English as a Second Language

To improve the grammatical skills of university-level students in an English as a Second Language (ESL) environment, the authors created a prototype software called GRAMSKIL. GRAM- SKIL differs from the current trend of software development in computer assisted language learning in two ways. Firstly, our program aims to develop grammatical competence instead of communicative competence in ESL learners. Secondly, it adopts the not-so-common approach of using a general purpose software tool—dBase III—to produce the program. GRAMSKIL uses the programming facility of dBase III to design menu-driven tasks which are user-friendly, and so computer novices can run the program without having to learn to run the database package. Moreover, GRAMSKIL allows teachers with little knowledge of database management systems to create their own database or modify the data to tailor them to the needs of their learners.     

基于WinCC V6.2的VB脚本操作自定义SQL数据库

针对工业项目中使用的SIMATICWinCC工业组态软件,利用WinCC集成的VB脚本可以很方便地操作Microsoft SQL Server中自定义数据库的特殊数据。避免了工业中使用WinCC组态软件在启动运行时要频繁地设置大量而复杂的参数,并且在人工设置参数后可以自动更新并存储于数据库中,以便下次运行时自动调用。     

Collecting Statistics over Runtime Executions

By collecting statistics over runtime executions of a program we can answer complex queries, such as “what is the average number of packet retransmissions” in a communication protocol, or “how often does process P₁ enter the critical section while process P₂ waits” in a mutual exclusion algorithm. We present an extension to linear-time temporal logic that combines the temporal specification with the collection of statistical data. By translating formulas of this language to alternating automata we obtain a simple and efficient query evaluation algorithm. We illustrate our approach with examples and experimental results.     

TOUGHREACT—A simulation program for non-isothermal multiphase reactive geochemical transport in variably saturated geologic media: Applications to geothermal injectivity and CO2 geological sequestration

TOUGHREACT is a numerical simulation program for chemically reactive non-isothermal flows of multiphase fluids in porous and fractured media. The program was written in Fortran 77 and developed by introducing reactive geochemistry into the multiphase fluid and heat flow simulator TOUGH2. A variety of subsurface thermo-physical–chemical processes are considered under a wide range of conditions of pressure, temperature, water saturation, ionic strength, and pH and Eh. Interactions between mineral assemblages and fluids can occur under local equilibrium or kinetic rates. The gas phase can be chemically active. Precipitation and dissolution reactions can change formation porosity and permeability. The program can be applied to many geologic systems and environmental problems, including geothermal systems, diagenetic, and weathering processes, subsurface waste disposal, acid mine drainage remediation, contaminant transport, and groundwater quality. Here we present two examples to illustrate applicability of the program. The first example deals with injectivity effects of mineral scaling in a fractured geothermal reservoir. A major concern in the development of hot dry rock and hot fractured rock reservoirs is achieving and maintaining adequate injectivity, while avoiding the development of preferential short-circuiting flow paths. Rock–fluid interactions and associated mineral dissolution and precipitation effects could have a major impact on the long-term performance of these reservoirs. We used recent European studies as a starting point to explore chemically induced effects of fluid circulation in the geothermal systems. We examine ways in which the chemical composition of reinjected waters can be modified to improve reservoir performance by maintaining or even enhancing injectivity. The second TOUGHREACT application example is related to CO₂ geologic sequestration in a saline aquifer. We performed numerical simulations for a commonly encountered Gulf Coast sediment under CO₂ injection conditions in order to analyze the impact of CO₂ immobilization through carbonate precipitation. Using the data presented in this paper, the CO₂ mineral-trapping capability after 10,000 years can reach 60 kg/m³ of sandstone by secondary carbonate mineral precipitation such as siderite, ankerite, and dawsonite. Most of the simulated mineral alteration pattern is consistent with the field observations of natural CO₂ reservoirs.     

SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins

SLDMOL is a program for modeling the 1-D scattering length density (SLD) profile of proteins at the lipid membrane–solution interface or adsorbed to other surfaces. The program reads experimental SLD data from neutron or X$X$-ray reflectivity measurements and compares the results to a trajectory of protein structures, finding the conformation and orientation that best fits the experimental data. SLDMOL is a freely distributed open source program written in python that can be run independently using command lines or a GUI. SLDMOL has also been integrated into the larger SASSIE package extending molecular modeling capabilities. Sample environment conditions can be replicated including H₂O/D₂O solvent contrasts, specific amino acid deuteration and complex molecular assemblies. Ensembles of protein conformations can be generated independently (e.g. molecular dynamics simulations) or with SASSIE. For each individual structure a best-fit SLD profile is outputted along with a goodness of fit parameter, protein depth penetration and surface coverage. In addition to individual comparisons SLD profiles can be calculated over ensemble averages of protein structures. As a result, SLDMOL provides a detailed molecular interpretation of reflectivity data or conversely can be used to predict experimental outcomes for different protein conformation and specific deuteration schemes prior to measurements.     

Perl-speaks-NONMEM (PsN)--a Perl module for NONMEM related programming

The NONMEM program is the most widely used nonlinear regression software in population pharmacokinetic/pharmacodynamic (PK/PD) analyses. In this article we describe a programming library, Perl-speaks-NONMEM (PsN), intended for programmers that aim at using the computational capability of NONMEM in external applications. The library is object oriented and written in the programming language Perl. The classes of the library are built around NONMEM's data, model and output files. The specification of the NONMEM model is easily set or changed through the model and data file classes while the output from a model fit is accessed through the output file class. The classes have methods that help the programmer perform common repetitive tasks, e.g. summarising the output from a NONMEM run, setting the initial estimates of a model based on a previous run or truncating values over a certain threshold in the data file. PsN creates a basis for the development of high-level software using NONMEM as the regression tool.     

Data race avoidance and replay scheme for developing and debugging parallel programs on distributed shared memory systems

Distributed shared memory (DSM) allows parallel programs to run on distributed computers by simulating a global virtual shared memory, but data racing bugs may easily occur when the threads of a multi-threaded process concurrently access the physically distributed memory. Earlier tools to help programmers locate data racing bugs in non-DSM parallel programs are not easily applied to DSM systems. This study presents the data race avoidance and replay scheme (DRARS) to assist debugging parallel programs on DSM or multi-core systems. DRARS is a novel tool which controls the consistency protocol of the target program, automatically preventing a large class of data racing bugs when the parallel program is subsequently run, obviating much of the need for manual debugging. For data racing bugs that cannot be avoided automatically, DRARS performs a deterministic replay-type function on DSM systems, faithfully reproducing the behavior of the parallel program during run time. Because one class of data racing bugs has already been eliminated, the remaining manual debugging task is greatly simplified. Unlike previous debugging methods, DRARS does not require that the parallel program be written in a specific style or programming language. Moreover, DRARS can be implemented in most consistency protocols. In this paper, DRARS is realized and verified in real experiments using the eager release consistency protocol on a DSM system with various applications.     

GIMMI: Geographic Information and Mathematical Models Inter-operability

GIMMI² project, started in April 2002, aims at bridging the gap of communication in the pesticide impact assessment domain between data providers (soil, meteorology, agronomy, pesticide experts), scientists (chemists, geologists, modellers and academic institutions), service providers (local and central governments, public administration bodies, private chemical industries manufacturing pesticides) and final users (agronomists, consultants and even citizens). This can be achieved by allowing the inter-operability via Web of Geographic Information Systems (GIS), environmental protection data and service (e.g. mathematical models) providers physically distributed, by providing the proper IT structures to represent and manage temporal knowledge, and by integrating state-of-the-art legacy systems for document management and report generation.The main results of GIMMI will be an open Web brokerage system supporting different web-services such as: On-line Data Access to seek and drill down into huge amount of distributed Geographic Information; On/Off-line Simulations allowing inter-relation of distributed databases to run mathematical models. “Open systems” means that new data and service providers can easily be integrated in the running system while remaining autonomous.The validation scenario chosen for GIMMI is the field of pesticides impact assessment in agriculture practices and Land Protection, by the adoption of four alternative EC-validated pesticide leaching models.     

Refinement of the thermodynamic modeling of the Nb–Ni system

The Nb–Ni system is reassessed on the basis of a critical literature review involving recent experimental data. These newly published experimental data include the phase relation associated with the NbNi₈ phase, phase transition temperatures resulting from selected alloys, all invariant reaction temperatures, and enthalpies of mixing of liquid, as well as the crystallographic data on the μ$\mu$ (Nb₇Ni₆) phase. A consistent thermodynamic data set for the Nb–Ni system is obtained by optimization of the selected experimental values. The calculated phase diagram, crystallographic properties and thermodynamic properties agree reasonably with the experimental data. Noticeable improvements have been made, compared with the previous thermodynamic optimizations.