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y = mccode(instr, options) : McCode (McStas/McXtrace) instrument


function y = mccode(instr, options)


 y = mccode(instr, options) : McCode (McStas/McXtrace) instrument

   iFunc/mccode a McCode instrument
     y=model instrument

       creates a model with specified McCode instrument 
       The instrument may be given as an '.instr' McCode description, or directly
       as an executable.
       requests a McCode file (*.instr,*.out) with a file selector.
 mccode('gui')   and 'mccode'  alone.
       list all available instruments in a list for a selection.
       uses templateDIFF.instr neutron powder diffractometer as example.
 mccode(description, options) also specifies additional McCode options, e.g.
   options.dir:         directory where to store results, or set automatically (string)
                          the last simulation files are stored therein 'sim'.
   options.ncount:      number of neutron events per iteration, e.g. 1e6 (double)
   options.mpi:         number of processors/cores to use with MPI on localhost (integer) 
                          when MPI is available, and mpi options is not given,
                          all cores are then used.
   options.machines:    filename containing the list of machines/nodes to use (string)
   options.seed:        random number seed to use for each iteration (double)
   options.gravitation: 0 or 1 to set gravitation handling in neutron propagation (boolean)
   options.monitor:     a single monitor name to read, or left empty for the last (string).
                        this can be a wildcard expression.
   options.mccode:      set the executable path to 'mcrun' (default, neutrons) or 'mxrun' (xrays)
   options.mpirun:      set the executable path to 'mpirun'
   options.compile:     0 or 1 to force re-compilation of the executable.
                          try that first if you can not create/use the object (old 
                          executable may be used).
   All options are stored and assignable in model.UserData.options.
   options can also be given as a string, e.g. 'ncount=1e6; monitor=*Theta*; compile=1'
   the 'monitor' option can also include further expressions, such as:
     options.monitor='*Theta*; signal=max(signal)/std(signal)^2;'

 The instrument parameters of type 'double' are used as model parameters. Other
 parameters (e.g. of type string and int) are stored in UserData.Parameters_Constant

 The options ncount, seed, gravitation, monitor can be changed for the model 
 evaluation, with e.g.:
   model.UserData.options.ncount     =1e5;
   model.UserData.options.monitor    ='*Theta*';

 Additional information is stored in the model.UserData, such as the instrument
 source, which you may view with:

   evaluates the model with given parameters (vector, cell, structure). Only
   scalar/double parameters of the instrument can be varied. Other parameters are kept fixed.
 model(p, nan) 
   evaluates the model and return the raw McCode data set (monitor).
 model(p, x,y,...) 
   evaluates the model and interpolates the McCode data set onto given axes.

 input:  p: variable instrument parameters (double, struct, char)
            p = [ double_type_instrument_parameters ]
         x,y,...: axes (double)

 output: y: monitor value
 ex:     model =mccode('templateDIFF'); 
         signal=iData(model, [], linspace(-10,100,100));
         signal=iData(model, [], nan); % to get the raw monitor

 To view the model geometry, use the mccode_display routine:
   model = mccode('templateDIFF');
   mccode_display(model, parameters)

 It is possible to scan model parameters when using vectors as value for the
 parameters. To achieve that, the parameter values must be given as a named 
 For instance, to scan the RV parameter in the templateDIF instrument, use:
   model = mccode('templateDIFF');
   p.RV= [ 0:.25:2 ];      % from 0 to 2 by steps of .25
   v=iData(model, p, nan); % we want the raw monitors as iData sets.

 To optimise instrument parameters, you should first fix the non-varying
 parameters, and possibly bound the others. Then the optimiser is launched
 with any 'fmax':
   model = mccode('templateDIFF');  % maximize
   fix(model, 'all'); model.RV='free';
   model.RV=[0 1 2];        % bounds and starting value
   p = fmax( model , [], '', nan)  % return the optimal parameters using the raw monitors

 Version: Aug. 22, 2017
 See also iFunc, iFunc/fits, iFunc/plot, iFunc/feval, mcstas
          <a href="http://www.mcstas.org">McStas</a>, <a href="http://www.mccode.org">McCode</a>
 (c) E.Farhi, ILL. License: EUPL.


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