auto mode

Auto mode is a simplified version of allin1, in which a single MEM run is used to first estimate the errors, and the user need not provide a parameter file for this error-estimation run. Instead, parameters are input for the second MEM run, and they are modified appropriately for estimation of the errors in the first run. This mode allows more user control than simple mode and is still easier to use than allin1 mode. For the first MEM run all standard errors are initially set to 1.0.

Although invert mode should be used with IGNORE = 2 for the analysis of Poisson kinetics (as in example 3 below), this new auto mode should suffice for nearly all other data (as in example 4 below). If the first two error estimates obtained in auto mode are quite different, an allin1 run with two or more error-estimation iterations can be done until the error estimates converge.

Here is a sample call to MemExp in auto mode:

memexp.exe auto invert.err.def data.001 1.0 analyze.def err1.dat err2.dat

Seven arguments follow the progam name on the command line when MemExp is run in auto mode. The first argument specifies the mode and is set to auto. The second argument, invert.err.def, is the name of the input file containing parameters to be used in the second inversion of the data using the time-dependent standard errors estimated from the first run. Only a few of these parameters are changed for use in the first inversion. The third, data.001, is the name of the data file to be inverted and may include the path of the file (the subdirectory where it is located). The fourth argument is a real number, D0, the data's normalization constant (equations 1, 2, 10, and 11). In the sample command line above, D0 is set to 1.0. The normalization of the fit is ultimately determined by the product of D0 and the integral of the lifetime distribution. Warning: Severely underestimating the normalization can induce spurious maxima in f [10]. The fifth argument, analyze.def, is the name of the input file containing parameters to be used in analyzing each of the MEM distributions automatically chosen by MemExp. This analysis involves writing the MEM fit and residuals to a file and revising the error estimates to be used for the next numerical inversion. The sixth and seventh arguments, err1.dat and err2.dat, are the names of the output files to which the kinetics data are written in three-column ( $t_i,y_i,\sigma_i$) format, along with the first and second estimates of time-dependent errors, respectively.

If WRNORM = T (true) in auto mode, the data's normalization, D0, is iteratively refined along with the error estimates: D0 is adjusted for use in the next MEM inversion according to the normalization of the distribution recommended by MemExp in the current inversion. When the normalization D0 is known (or not to be changed by the program), set WRNORM to F (false) to avoid this adjustment of D0 in auto mode.