Configuration
-------------

Input
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The users need to use a YAML file to specify the parameters used for the
generation of the phase diagram and calculation of the critical point.
The current input file has seven sections that need to be specified. In
practice, the users only need to specify the section: model_type. Other
sections will be filled with default parameters. The users can also choose
to specify them if they don't want to use the default parameters.

The first section is to choose the model. The model can either be
polynomial_hyperbolic, or muses_parametric. As an example, here the model is
chosen to be the polynomial hyperbolic model, specified as follows in the yaml
input file:

::

   model_type: polynomial_hyperbolic

The second section is the output, which determines where and in what format
the output files are generated. The EoS tables are written as CSV files in the
folder named by output_path, and a summary YAML file named by yaml_output_file
records the run metadata. We allow the user to choose the format of the output
tables. If one chooses the format to be "muses-synthesis", then the table would be in the standard
MUSES format for the Synthesis module, which is headerless. If one chooses the format to be "legacy",
the tables will include a detailed header with descriptions for each column. For
MUSES format, one can decide what extra columns they want to include by specifying
the variable muses_extra_columns:

::

   output_options:
       yaml_output_file: muses_polyhyperbolic_bestfit.yaml
       output_path: muses_polyhyperbolic_bestfit
       format: muses-synthesis
       muses_extra_columns: ["chi2_B","dsdTfmu","drho_BdTfmu","dsdmufT"]

The third section is for the generation of the phase diagram:

::

   eos_options:
       eos_stages:
           interpolate_points: true
           maxwell_construction: true

       temperature_options:
           T_min: 20
           T_max: 400
           T_step: 2.5
           N_phi0_lines: 200

       chemical_potential_options:
           mu_B_min: 0
           mu_B_max: 2000
           mu_B_step: 5
           N_Phi1_lines: 1000

The fourth section configures the transport coefficient calculation. When
``transport_coefficient: true``, the code solves the full coupled system of background
and perturbative ODEs (19 states) and appends transport quantities as extra columns in
the output. When ``transport_coefficient: false`` (or omitted), the code only solves the
background ODE system (11 states), which is significantly faster and sufficient for
EoS-only calculations. The ``velocity`` parameter is used for the energy-loss calculations
and may be a single value or a list of values between :math:`0.01` and :math:`0.99`.
::

   transport_options:
      transport_coefficient: true
      velocity: 0.5

The fifth section is for the calculation of the critical points,
which is not implemented in the current version.
::

   critical_point_options:
       yaml_output: critical_point_interp.yaml
       phi0_min: 0.5
       phi0_max: 10
       N_lines: 800
       max_tries: 1000
       initial_Phi1_step: 1e-5
       max_Phi1_step: 0.2
       prec_T: 0.0001
       prec_mu: 0.0001
       acc_T: 0.001
       acc_mu: 0.001

The sixth section is the parameters for the polynomial hyperbolic model.
If the users choose the polynomial hyperbolic model, the best parameter set
determined from Bayesian analysis will be used by default and listed below.
If the users want to choose their own parameters, they can change the related
fields. If the users choose to use muses parametric model and specified it in
the section model_type, this section will be ignored by the code:
::
   polynomial_hyperbolic:
      parameters:
      description: Parameters of the model in question.
      flag_default: no
      Lambda: 1148.121631179041
      kappa2: 11.350245262021625
      gamma: 0.5884489971316446
      b2: 0.301821894469367
      b4: -0.04261907765391285
      b6: 0.0004566058948051932
      c1: -0.06469185351673243
      c2: -0.22517557265138566
      c3: 0.03664412474454205
      d1: 1.7231476382001352
      d2: 472.2764686476346

The seventh section is the parameters for the muses parametric model.
If the users choose the muses parametric model, the best parameter set
determined from Bayesian analysis will be used by default and listed below.
If the users want to choose their own parameters, they can change the related
fields. If the users choose to use muses parametric model and specified it in
the section model_type, this section will be ignored by the code:
::
   muses_parametric:
      parameters:
         A: 0.371277835493431
         Dphi1: 0.0002961963589748086
         Dphi2: 0.6875695068406373
         DphiV: 1.79170830255505
         Lambda: 955.0262652764986
         flag_default: false
         kappa2: 11.435350223991247
         phi1: 0.0021558487922312113
         phi2: 2.1826170630756385
         slope1: 0.5216148015697675
         slope2: 0.6111004602504531