Manual page for apps.StatPhys program

StatPhys calculates various thermodynamic properties as a function of temperature from a density of states and measured observables

-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 StatPhys 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
-mute suppress all messages from a given package or class, e.g. “-mute=jbcl.data.formats”, or “-mute=jbcl.calc.structural.Crmsd”. It is also possible to switch of a whole branch from the jbcl library, e.g. “-mute=jbcl.data” will mute all comming from jbcl.data.formats,jbcl.data.types, jbcl.data.dict and jbcl.data.basic. To switch all the messages, say: “-mute=jbcl” or simply “-mute” because the default behaviour is to mute everything. This option is executed AFTER -verbose, so user may increase verbosity level to a desired valueand then selectively switch off logging from some packages
-statphys.in.density=<file name> input DOS (two column format: E, Omega[E]
-statphys.in.energies=<file name> input energy values
-statphys.in.observations=<file name> input observable values
-statphys.o_max=<value> highest value of the canonical observable
-statphys.o_min=<value> lowest value of the canonical observable
-statphys.o_step=<value> step used to tabulate canonical observable
-statphys.out.overlap=<file name> calculates overlap betwen any two energy ditributions as a function of temperarture q(T_i,T_j) and saves results into a file
-statphys.out.pet=<file name> runs P(E|;T) calculations and stores the result in a file
-statphys.out.poe=<file name> runs P(O,E) calculations and stores the result in a file
-statphys.out.pot=<file name> runs P(O|;T) calculations and stores the result in a file
-statphys.out.rex=<file name> calculates replica exchange probability as a function of temperarture r(T_i,T_j) and saves results into a file
-statphys.t_max=<value> highest temperature value
-statphys.t_min=<value> lowest temperature value
-statphys.t_step=<value> temperature step
-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.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 the density of states for a system and tabulate basic
thermodynamic quantitieswithin a given range of temperatures.
    java apps.StatPhys -statphys.in.density=omega -statphys.t_min=285 -statphys.t_max=325 -statphys.t_step=1.0