Manual page for apps.WHAM program

WHAM program reads a file with multiple columns and computes the density of states.

-h print a brief summary of available options
-help=<name-part> print a help message on the screen - ANSI terminal version with visual enhancements. If <name-part> argumen is given, the program will print only these options that contains that substring
-help.dox=<name> print a help message in doxygen (*.dox) format on the screen for the WHAM program
-help.md=<name> print a help message in markdown (*.md) format on the screen
-help.option=<option-name> print a help message for a single option on the screen.
-help.plain=<name-part> print a help message on the screen - plain text version. If <name-part> argumen is given, the program will print only these options that contains that substring
-in.fname=<file name> provides a name of a file with input data
-in.fnames=<file names> provides a number of input file names
-out.fname=<file name> provides an output file name
-verbose=<integer> Sets up a verbosity level to a given value. The argument should be an integer from the rangefrom 0 (no messages at all, which is equivalent to -mute=jbcl) to 6 when everything is logged. See -mute for additional information.
-wham.b=<values> Provide a vector of inverse temperature (beta) values at which the energy was observed The number of T values much math the number of energy columns
-wham.bin_width=<value> with for an energy bin
-wham.epsilon=<value> stop criteria for WHAM iterations
-wham.n_bins=<value> with for an energy bin
-wham.t=<values> Provide a vector of temperature values at which the energy was observed The number of T values much math the number of energy columns

EXAMPLES

      (1) Read energy observations from a file and calculate the density of
states for a system. WHAM will use provided temperature values; energy
bin width is 0.25
    java apps.WHAM -i=energy.dat -t=0.1,0.2,0.5,1.0,2.0,5.0 -w=0.25