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3. Keywords

The input file for Normal is an ascii text file containing keywords and values associated with those keywords. A simple syntax is used. Keywords and their values are delimited by white spaces, where white space can be any number of spaces or tabs and one comma (,) or equals sign (=). Most keywords have one value associated with them. The keyword files is special. It must be the last keyword in the input file and it precedes the list of files containing data to be normalized and aligned. Each filename following the files keyword must be on its own line. See the appendix for an example input file.

3.1 A Brief List of the Keywords

  1. !, %, # characters denoting comments
  2. outfile name of output file
  3. format i/o file format
  4. formin input file format
  5. formout output file format
  6. e0 edge energy of standard
  7. ee edge energy of standard
  8. pre1 beginning energy for pre-edge subtraction
  9. pre2 end energy for pre-edge subtraction
  10. nor1 beginning energy for normalization
  11. nor2 end energy for normalization
  12. emax end energy for alignment fit
  13. nofit flag to only normalize data
  14. noalign flag to only normalize data
  15. derivative flag to calculate and write derivative function
  16. norm flag to only normalize data
  17. end flag to end reading input file
  18. files flag indicating that data filenames follow

3.2 Full Explanation of Keywords

!, %, and #

These characters denote comments in the input file. Anything on a line following any one of these characters will be ignored.

Outfile

This is the name for the file(s) containing the aligned data. If no output file name is specified, the input file name will be used with the extension changed to nor or with _norm added to the filename. The file extension is defined as all characters after the final dot (.) in the file name. This definition meets the definition of an extension in DOS and VMS, and is well defined in a Unix environment.

Format, Formin, Formout

These specify the formats for the input and output data files. By default, files are read in the ASCII format. The other option is the UWXAFS format. The format keyword specifies both input and output format. Note that the input and output formats do not need to be the same.

e0, ee

This specifies the edge energy of the standard data set.

pre1, pre2

These specify the beginning and end values of the energy range to be used for the pre-edge subtraction. These values are relative to the edge energy, e0, as specified in the input file. Their default values are -200 and -50, respectively. Note that pre1 is lower in energy than pre2.

nor1, nor2

These specify the beginning and end values of the energy range to be used for the normalization. These values are relative to the edge energy, e0, as specified in the input file. Their default values are 100 and 500, respectively. Note that nor1 is lower in energy than nor2.

emax

This specifies the largest energy value used in the alignment fit. The value is relative to the edge energy, e0, as specified in the input file. If unspecified, it is the last energy point in the standard or in the data, whichever is smaller. If there are features in either the standard or the data that might bias the fit, for instance glitches or Bragg peaks, it may improve the quality of the alignment to specify emax such that these features are avoided. Generally, however, the default for emax should produce the most reliable alignment.

nofit, noalign, norm

These keywords are synonymous. They are flags telling Normal to skip the alignment fit and only normalize the input data. These keywords take no value, simply placing one in the input file tells the code to skip the alignment. The default is to align the data.

derivative

This keyword is a logical flag telling Normal to calculate the derivative of the normalized data. This keyword takes no value, simply placing it in the input file tells the code to perform this calculation. The default is to not calculate and write the derivative functions.

end

When this keyword is encountered in the input file, Normal will stop reading the input file and begin processing the data. Everything after this keyword in the input file will be ignored. This keyword takes no value.

files

This keyword tells Normal to go to the next line and begin reading the names of the input data files. This must be the last keyword in the input file. Each input filename must be on its own line. Every thing on the line after the filename is assumed to be a comment unique to that data set. This comment will be written to the header of the output data file. If the UWXAFS binary format is used for the input data, the nkey or skey follow the filename and everything after the key is assumed to be the comment. If the comment begins with one of the comment characters then it will be ignored and not written to the header of the output file.


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