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Redesign userinput

  • Set default values for all fields (if there is really no good default for some fields, make them mandatory).

  • Remove Suffix _i from all fields

  • Rename userinput -> UserInput or Userinput (Naming conventions). Also apply naming conventions to all fields.

  • Make the class a data only struct without constructor. Benefit: Can now do direct initialization

    const auto userinput = UserInput{ .N_zones = 1, .constrained_direction = 1, ... };

  • Move readParametersXMLFile out of the class / struct, replacing it with UserInput load_user_input(const std::filesystem::path &path)

  • Use std::optional instead of boolean flag, value pairs wherever possible

    • read_restart and restart_file_name can be combined
    • save_restart_files and restart_files_frequency can be combined Drop those unused fields
    • save_output_files and output_files_frequency can be combined
    • onsager_coefficient, dt_transport_coeff and heat_rate_tolerance_per_atom are used only if thermal_transport_flag is true Drop field thermal_transport_flag
    • UseOpenKIM and ModelName can be combined
    • MEAMPotential, MEAMLibraryFile and MEAMParameterFile can be combined
    • mid_FIRE_output_flag and mid_FIRE_output_frequency can be combined
    • we can combine periodic, minimum, period_length and constrain_periodic_relaxation

  • Use std::filesystem::path for paths

  • Make userinput a cmake module

  • Warn about invalid field names in input file

  • Change type of external_displacement_gradient_i from std::array<double, 9> -> std::array<std::array<double, 3>, 3>

  • replace xml by json. New file would look like:

    {
  "DomainAndMeshGeneration": {
    "x_char": 1.7649832125,
    "N_zones": 0
  },
  "SolverTolerances": {
    "MaxForceResiduePerAtom": 1.0e-6,
    "MaxThermalForceResiduePerAtom": 1.0e-6,
    "MaxPeriodicForceResiduePerAtom": 1.0e-6
  },
  "SimulationSettings": {
    ...
    "X periodic": true,
    ...
    "fixed_box_upper": [125.0, 13.264, 40.0],
    ...
  },
  ...
}

    Compared to xml:

    <UserInputParameters Version="0.1"> 	
 <DomainAndMeshGeneration> 
   <Fields>
     <Field Name="x_char"> 1.7649832125 </Field> 
     <Field Name="N_zones"> 0 </Field>
   </Fields> 
 </DomainAndMeshGeneration>

 <SolverTolerances> 
   <Fields>
     <Field Name="MaxForceResiduePerAtom"> 1.0e-6 </Field> 
     <Field Name="MaxThermalForceResiduePerAtom"> 1.0e-6 </Field>
     <Field Name="MaxPeriodicForceResiduePerAtom"> 1.0e-6 </Field>
   </Fields> 
 </SolverTolerances>

 <SimulationSettings> 
   <Fields>
     ...
     <Field Name="X periodic"> true</Field>
     ...
     <Field Name="fixed_box_upper"> 125.0, 13.264, 40.0 </Field>
     ...
   </Fields> 
 </SimulationSettings> 
 ...
</UserInputParameters>

    Benefits:

    • support for lists [], true, false, null (<-> std::optional) supported by the format.
    • Compacter files
    • json is more lightweight than xml -> less complex parsing using nlohmann_json

  • write a JSON schema that helps with editing, and we could also use it to check the JSON

  • Provide an xml -> json converter to make migration smooth

Open tasks:

  • Review (@webmanue), comments (@ssaxena, @mspinola) on whether some input parameters only make sense for activated features (and could be combined into a std::optional)
  • Make sure the new dependency nlohmann_json works on Euler
Edited by brgerhar