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DynaFit
Scripting Manual
ver. 3.28
Petr Kuzmi
, Ph.D.
- Introduction
- General Considerations
- Formatting of the script files
- Sections
- Keywords
- Ranges and sets of values
- Concentration and time scale
- Optimized parameters
- Multiple tasks
- Output files
- Initialization files
- Mechanism
- Molecularity and reaction order
- Chemical notation
- Arrows
- Species names
- Rate and equilibrium constant names
- Constant rates in open reaction systems
- Kinetic Constants
- Concentrations
- Concentration scale
- Global and local concentrations
- Local concentrations
- Concentrations as optimized parameters
- Linked concentrations
- Arbitrary linking factor
- Specific molar responses
- Global response coefficients
- Local response coefficients
- Difference response coefficients
- Analysis of reaction velocities
- Progress Curves
- Data files
- Local vs. global analysis
- Simulation mesh
- Experimental error
- Mixing delay time
- Offset
- Local concentrations
- Local response coefficients
- Concentration jump experiments
- Keyword ordering
- Velocities
- Molar response coefficients
- Rapid-equilibrium vs. dynamic methods
- Location of data files
- Experimental error
- Diagnostic plots
- Equilibria
- `Sweeping' rate constant values
- Initialization file
- Initialization file
- Control parameters
- <ODE Solver>
- Iterations = Maximum number of LSODE iterations
- AbsTolerance = Absolute tolerances for local truncation error
- RelTolerance = Relative tolerances for local truncation error
- AbsAccurateTol = Enhanced absolute tolerances for local truncation error
- RelAccurateTol = Enhanced relative tolerances for local truncation error
- NonNegative = Non-negativity flag for ODE solution
- SmartWeighting = Flag for automatic error tolerances
- <Equilibrium Solver>
- <Marquardt>
- Iterations = Number of iterations
- Subiterations = Number of sub-iterations
- Interrupt = Number of iterations before switching to interactive mode
- Restarts = Number of times the LM algorithm should restart
- InitLambda = Initial value of the Marquardt compromise parameter
- UpLambda = Increase in the Marquardt compromise parameter
- DownLambda = Decrease in the Marquardt compromise parameter
- ReinitLambda = Reinitialization flag for the Marquardt compromise parameter
- StepLine = Number of steps in a line-search algorithm
- StrideLine = Initial step size in the line-search algorithm
- IterPrint = Printing of major iterations in the LM algorithm
- SubiterPrint = Printing of minor iterations in the LM algorithm
- FilePrint = Logging the progress of the LM minimization in a disk file
- ShowProgress = Displaying the progress of the LM minimization on the screen
- StopLambda = Stopping criterion for the Marquardt compromise parameter
- StopParam = Stopping criterion for adjustable parameters
- StopSquares = Stopping criterion for the reduced sum of squares
- <Confidence Intervals>
- <Constraints>
- RateErrAbsRel = Flag for absolute or relative bounds
- RateError = Optimization bounds for rate constants
- RateStopAbsRel = Flag for absolute or relative stopping criterion
- RateStop = Stopping criterion for rate constants
- ConcErrAbsRel = Flag for absolute or relative bounds
- ConcError = Optimization bounds for concentrations
- ConcStopAbsRel = Flag for absolute or relative stopping criterion
- ConcStop = Stopping criterion for concentrations
- RespErrAbsRel = Flag for absolute or relative bounds
- RespError = Optimization bounds for molar responses
- RespStopAbsRel = Flag for absolute or relative stopping criterion
- RespStop = Stopping criterion for molar responses
- OffsErrAbsRel = Flag for absolute or relative bounds
- OffsError = Optimization bounds for baseline offsets
- OffsStopAbsRel = Flag for absolute or relative stopping criterion
- OffsStop = Stopping criterion for baseline offsets
- <Simulate>
- Sensitivity = Flag for the simulation of parametric sensitivities
- MeshDefault = Number of points on a simulated curve
- Equalize = Flag for equal weighting of data sets
- FiniteDifference = Finite-difference coefficient
- Interpolate = Flag for interpolation of progress curves
- Increment = Time increment in the interpolation of progress curves
- WaitBatch = Time delay in batch simulations
- <Filter>
- <Output>
- CreateDirectories = Create output directories?
- WriteTextFiles = Create output files in simple text format?
- WriteHTMLfiles = Create output files in HTML format?
- WriteLATEXfiles = Create output files in LaTeX format?
- WriteGIFfiles = Create graphical output files in GIF format?
- WritePSfiles = Create graphical output files Postscript format?
- WriteTABfiles = Create output files in tab-delimited format?
- TextFileCreator = Text file creator string
- PostscriptFileCreator = Postscript file creator string
- WriteStoich = Write stoichiometric and formula matrices?
- VarianceInflation = Print variance inflation factors?
- Covariance-Correl = Print variance-covariance matrix?
- CollinearityIndex = Print collinearity index?
- Eigenvectors = Print eigenvalues and eigenvectors?
- RedundancyGrade = Print redundancy grade?
- Variance-Signal = Plot best-fit signal value vs. squared deviations?
- CumulativeDistrib = Plot empirical cumulative distribution of residuals?
- NormalPlot = Produce cumulative normal plot?
- SerialCorrelation = Produce serial correlation plot of residuals?
- AutoCorrelation = Produce autocorrelation plot of residuals?
- PowerSpectrum = Produce power spectrum using Fast Fourier Transform?
- LocalResid = Combine residuals from multiple data sets?
- RunsOfSigns = Compute the runs-of-signs test for residuals?
- Rayner-Best = Compute the Rayner-Best statistics for residuals?
- Kolmogorov-Smirnov = Compute the Kolmogorov-Smirnov statistics for residuals?
- Durbin-Watson = Compute the Durbin-Watson statistics for residuals?
- Tukey = Compute the Tukey statistics for residuals?
- WriteFTest = Perform model discrimination analysis using Fisher's
-statistic?
- <Plot>
- IndependentVar = Label for independent variable
- DependentVar = Label for dependent variable
- HighResolution = High-resolution graphic output?
- WaitLocal = User input during local analysis of progress curves?
- ClickGraphs = Wait for user input upon displaying graphics?
- WaitTime = Time for display of output graphs
- XPixels = Number of pixels in the horizontal direction
- YPixels = Number of pixels in the vertical direction
- ScreenColumns = X-Dimension of the ASCII plot (screen)
- ScreenRows = Y-Dimension of the ASCII plot (screen)
- FileColumns = X-Dimension of the ASCII plot (file)
- FileRows = Y-Dimension of the ASCII plot (file)
- ShowXResiduals = Plot residuals against independent variable?
- ShowYResiduals = Plot residuals against dependent variable?
- ResidRange = Range of Studentized residuals
- TMinVelocity = Minimum time for plotting velocities
- <Velocity>
- AutoWrite = Flag for recording initial velocities on disk
- WriteFittedConc = Flag for writing optimized concentrations
- AverageInput = Flag for averaging of replicates
- AlwaysPositive = Flag for positive velocities
- ExcludeOutliers = Flag for the exclusion of outliers
- MinimumPoints = Smallest number of replicates
- StandardDeviation = Criterion for the exclusion of outliers
- <ODE Solver>
- Bibliography
- List of Figures
- List of Tables
- Index
iteractions
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Petr Kuzmic | Jul 12 2005