Example Input File

The input file example used here is taken from moltres/problems/MooseGold/033117_nts_temp_pre_parsed_mat/auto_diff_rho.i. Before delving into the file, we note that all the parameter options for different input blocks can be seen by executing moltres-opt --dump.

Ok, from the top:

 flow_velocity=21.7 # cm/s. See MSRE-properties.ods nt_scale=1e13 ini_temp=922 diri_temp=922 

Variables defined at the top of an input file can be used throughout the remainder of the file with GetPot syntax. We will show later in the input file an example of the GetPot syntax. Following the GetPot variables definitions, we have the GlobalParams block:

 [GlobalParams] num_groups = 2 num_precursor_groups = 6 use_exp_form = false group_fluxes = 'group1 group2' temperature = temp sss2_input = false pre_concs = 'pre1 pre2 pre3 pre4 pre5 pre6' account_delayed = true [] 

In GlobalParams, parameters like num_groups can be globally set to a value. Consequently any class (e.g. the kernel class GroupDiffusion) that has the parameter num_groups will read in a value of 2 unless it is overridden locally in its input block. It should be noted that the GlobalParams block and any other MOOSE input block can be placed anywhere in the input file; at execution time each block will be read when appropriate. Parameters description:

• num_groups: The number of energy groups for neutron diffusion
• num_precursor_groups: The number of delayed neutron precursor groups
• use_exp_form: Whether the actual neutron/precursor fluxes/concentrations should be represented by $u$ or $e^u$ where $u$ is the actual variable value
• group_fluxes: The names of the neutron group fluxes
• temperature: The name of the temperature variable
• sss2_input: True if the macroscopic group constants were generated by Serpent 2. False otherwise
• pre_concs: The names of the precursor concentration variables
• account_delayed: Whether to account for delayed neutron production. Modifies the neutron source term

Following GlobalParams in our example, we have the Mesh block:

 [Mesh] file = '2d_lattice_structured.msh' # file = '2d_lattice_structured_jac.msh' [] 

Before describing the Mesh block, we note that comments in the Moltres input file can be introuduced with the # character. Any characters following the # character will not be read by the MOOSE parser.

The two most commonly used Mesh types are FileMesh and GeneratedMesh. The Mesh input block by default assumes type FileMesh and takes a parameter argument file = <mesh_file_name>. Many MOOSE users generate their meshes using Cubit/Trellis. For national lab employees this software is free; however, academic or industry users must pay. Consequently, Moltres meshes to date have been generated using the software gmsh which is free and open source. Binaries for Windows, Mac, and Linux as well as source code can be downloaded here. Ubuntu users may also install gmsh using sudo apt-get install gmsh. We will not go into the details of using gmsh but the interested user should peruse its documentation. There are many example gmsh input files in the Moltres repository (denoted by the .geo extension). To generate a mesh for use with Moltres, a typical bash command is gmsh -2 -o file_name.msh file_name.geo where 2 should be replaced with the dimension of the mesh, the argument following -o is the name of the output .msh file, and the last argument is the input .geo file.

Gmsh or Cubit can be used for generation of highly complex mesh structures. However, if the user just wishes to generate a simple mesh, he/she may use MOOSE’s built-in type GeneratedMesh. For using GeneratedMesh we refer the reader here.

Next in our example input file, we have the Problem block:

 [Problem] coord_type = RZ [] 

The Problem block may usually be omitted from the input file for a Cartesian simulation. However, since this particular example is using 2D-axisymmetric coordinates, we have to convey this information using Problem’s coord_type parameter.

The Variables block introduces sub-blocks:

 [Variables] [./group1] order = FIRST family = LAGRANGE initial_condition = 1 scaling = 1e4 [../] [./group2] order = FIRST family = LAGRANGE initial_condition = 1 scaling = 1e4 [../] [./temp] initial_condition = ${ini_temp} scaling = 1e-4 [../] []  Sub-blocks are initialized with [./<object_name>] and closed with [../]. The group1 sub-block creates a MooseVariable object with the name group1. The family parameter describes the shape function type used to form the approximate finite element solution. The order parameter denotes the polynomial order of the shape functions. initial_condition is an optional parameter that can be used to set a spatially uniform initial value for the variable. scaling is another optional parameter that can be used to scale the residual of the corresponding variable; this is usually done when different variables have residuals of different orders of magnitude.  [PrecursorKernel] var_name_base = pre block = 'fuel' outlet_boundaries = 'fuel_tops' u_def = 0 v_def =${flow_velocity} w_def = 0 nt_exp_form = false family = MONOMIAL order = CONSTANT # jac_test = true [] 

Whereas all the other blocks that have been introduced are standard MOOSE blocks, PrecursorKernel is a custom input file block unique to Moltres. The PrecursorKernel action creates all the precursor variables, kernels, and boundary conditions necessary for solving the precursor governing equations. Parameter descriptions:

• var_name_base: The prefix for the precursor variable names. Name suffixes are numbers, e.g. pre1, pre2, ...
• block: This is a parameter ubiquitous to many MOOSE classes such as kernels and materials. By specifying a value for block the user is asking that in this case, precursors and their associated governing equations only be solved for in the fuel mesh subdomains
• outlet_boundaries: The mesh boundaries from which the precursors flow out
• u_def, v_def, w_def: The x, y, and z components of velocity, or in the case of an RZ simulation, u_def is the r velocity component, v_def is the z-component, and w_def has no meaning
• nt_exp_form: Whether the neutron group fluxes have their concentrations in an exponential form. If use_exp_form is false in the GlobalParams block, this should also be false
• jac_test: true if testing the application developer’s jacobian against a jacobian formed through finite differencing of the residuals. Defaults to false.

 [Kernels] # Neutronics [./time_group1] type = NtTimeDerivative variable = group1 group_number = 1 [../] [./diff_group1] type = GroupDiffusion variable = group1 group_number = 1 [../] [./sigma_r_group1] type = SigmaR variable = group1 group_number = 1 [../] [./fission_source_group1] type = CoupledFissionKernel variable = group1 group_number = 1 [../] [./delayed_group1] type = DelayedNeutronSource variable = group1 [../] [./inscatter_group1] type = InScatter variable = group1 group_number = 1 [../] [./diff_group2] type = GroupDiffusion variable = group2 group_number = 2 [../] [./sigma_r_group2] type = SigmaR variable = group2 group_number = 2 [../] [./time_group2] type = NtTimeDerivative variable = group2 group_number = 2 [../] [./fission_source_group2] type = CoupledFissionKernel variable = group2 group_number = 2 [../] [./inscatter_group2] type = InScatter variable = group2 group_number = 2 [../]

# Temperature [./temp_time_derivative] type = MatINSTemperatureTimeDerivative variable = temp [../] [./temp_source_fuel] type = TransientFissionHeatSource variable = temp nt_scale=${nt_scale} block = ‘fuel’ [../] # [./temp_source_mod] # type = GammaHeatSource # variable = temp # gamma = .0144 # Cammi .0144 # block = ‘moder’ # average_fission_heat = ‘average_fission_heat’ # [../] [./temp_diffusion] type = MatDiffusion D_name = ‘k’ variable = temp [../] [./temp_advection_fuel] type = ConservativeTemperatureAdvection velocity = ‘0${flow_velocity} 0’ variable = temp block = ‘fuel’ [../] [] 

The Kernels block is pretty straightforward. The kernel type or class is specified with type = <kernel_type>. The mathematical representation of each Moltres kernel type can be found on the kernel wiki page. Each kernel contributes to the residual of the variable specified by variable = <variable_name>. Kernels can be optionally block restricted by setting block = <subdomain_names>.

 [BCs] [./vacuum_group1] type = VacuumConcBC boundary = 'fuel_bottoms fuel_tops moder_bottoms moder_tops outer_wall' variable = group1 [../] [./vacuum_group2] type = VacuumConcBC boundary = 'fuel_bottoms fuel_tops moder_bottoms moder_tops outer_wall' variable = group2 [../] [./temp_diri_cg] boundary = 'moder_bottoms fuel_bottoms outer_wall' type = FunctionDirichletBC function = 'temp_bc_func' variable = temp [../] [./temp_advection_outlet] boundary = 'fuel_tops' type = TemperatureOutflowBC variable = temp velocity = '0 ${flow_velocity} 0' [../] []  The BCs block is very similar to the Kernels block except the boundary = <boundary_names> parameter must be specified to indicate where the boundary conditions should be applied. The mathematical form of the BCs can be found on the BCs wiki page.  [Functions] [./temp_bc_func] type = ParsedFunction value = '${ini_temp} - (${ini_temp} -${diri_temp}) * tanh(t/1e-2)' [../] [] 

The Functions block is necessary when other MOOSE/Moltres objects specified in the input file require functions. In this example we have a boundary condition object temp_diri_cg of type FunctionDirichletBC that requires a function object to specify the values of the variable temp along the reactor boundaries. We name this function object temp_bc_func and specify it to be of type ParsedFunction which is a function type that can be written in terms of constants and the independent variables $x, y, z$ and $t$. Here we see the use of GetPot syntax ${<variable_name>}$ to access the values of ini_temp and diri_temp specified at the top of the input file.

 [Materials] [./fuel] type = GenericMoltresMaterial property_tables_root = '../property_file_dir/newt_msre_fuel_' interp_type = 'spline' block = 'fuel' prop_names = 'k cp' prop_values = '.0553 1967' # Robertson MSRE technical report @ 922 K [../] [./rho_fuel] type = DerivativeParsedMaterial f_name = rho function = '2.146e-3 * exp(-1.8 * 1.18e-4 * (temp - 922))' args = 'temp' derivative_order = 1 block = 'fuel' [../] [./moder] type = GenericMoltresMaterial property_tables_root = '../property_file_dir/newt_msre_mod_' interp_type = 'spline' prop_names = 'k cp' prop_values = '.312 1760' # Cammi 2011 at 908 K block = 'moder' [../] [./rho_moder] type = DerivativeParsedMaterial f_name = rho function = '1.86e-3 * exp(-1.8 * 1.0e-5 * (temp - 922))' args = 'temp' derivative_order = 1 block = 'moder' [../] [] 

In the Materials block we specify materials that live on a mesh subdomain. Any given subdomain can have as many materials as desired. An important material in Moltres is GenericMoltresMaterial. Its parameters:

• property_tables_root: The path and prefix of the files that contain the macroscopic group constants that define neutron reaction rates
• interp_type: The type of fitting/interpolation to be carried out on the temperature grid. Options are:
• bicubic_spline: Done when macroscopic constants are a function of the temperature of the local material as well as the average temperature of the other material
• spline: Most common option used for monovariate interpolation between temperature knots
• least_squares: Constructs a linear fit function of macroscopic constants as a function of temperature. Useful when group constant interpolation table is not monotonic
• none: Only should be used when single values for constants are supplied at a single temperature
• prop_names, prop_values: name-value pairs used to define material property values from the input file. In this example, both the thermal conductivity $k$ and the specific heat capacity $c_p$ are defined from the input file for both fuel and moderator subdomains.

DerivativeParsedMaterial is a material inherited from the Phase Field module of the MOOSE framework. Its useful for creating material properties that are functions of solution variables and for coupling the dependency of the property on the variable back into the Jacobian used for Newton-Raphson. A more in-depth description of the material along with its relatives is given here.

 [Executioner] type = Transient end_time = 10000

nl_rel_tol = 1e-6 nl_abs_tol = 1e-6

solve_type = ‘NEWTON’ petsc_options = ‘-snes_converged_reason -ksp_converged_reason -snes_linesearch_monitor’ petsc_options_iname = ‘-pc_type -sub_pc_type -pc_asm_overlap -sub_ksp_type -snes_linesearch_minlambda’ petsc_options_value = ‘asm lu 1 preonly 1e-3’ # petsc_options_iname = ‘-snes_type’ # petsc_options_value = ‘test’

nl_max_its = 30 l_max_its = 100

dtmin = 1e-5 # dtmax = 1 # dt = 1e-3 [./TimeStepper] type = IterationAdaptiveDT dt = 1e-3 cutback_factor = 0.4 growth_factor = 1.2 optimal_iterations = 20 [../] []

[Preconditioning] [./SMP] type = SMP full = true [../] [] 

The Executioner and Preconditioning blocks are essential to determining the method used to solve the system of non-linear equations created by finite element discretization of our molten salt reactor governing equations. Executioner and Preconditioning documentation can be found here and here respectively.

 [Postprocessors] [./group1_current] type = IntegralNewVariablePostprocessor variable = group1 outputs = 'console csv' [../] [./group1_old] type = IntegralOldVariablePostprocessor variable = group1 outputs = 'console csv' [../] [./multiplication] type = DivisionPostprocessor value1 = group1_current value2 = group1_old outputs = 'console csv' [../] [./temp_fuel] type = ElementAverageValue variable = temp block = 'fuel' outputs = 'csv console' [../] [./temp_moder] type = ElementAverageValue variable = temp block = 'moder' outputs = 'csv console' [../] # [./average_fission_heat] # type = AverageFissionHeat # nt_scale = \${nt_scale} # execute_on = 'linear nonlinear' # outputs = 'console' # block = 'fuel' # [../] [] 

General postprocessor documentation can be found here. In this example, the first three postprocessors group1_current, group1_old and multiplication are used to calculate the neutron multiplication between current and old timesteps. The IntegralNewVariablePostprocessor integrates the supplied variable’s value over the entire domain at the current time step. The IntegralOldVariablePostprocessor does the same thing but for the previous time-step. The DivisionPostprocessor then divides value1 by value2. The ElementAverageValue postprocessor simply calculates the average value of a variable over an optionally restricted domain. AverageFissionHeat, commented out in this example, determines the average volumetric fission heating rate over a domain. This has been used to implement gamma radiation heating in the moderator as some fraction of the average fission heat produced in the fuel.

 [Outputs] print_perf_log = true print_linear_residuals = true csv = true [./out] type = Exodus [../] [] 

Outputs documentation is here.

 [Debug] show_var_residual_norms = true [] 

This simply tells our executable to print the variable residual norms during the non-linear solve.

 # [ICs] # [./temp_ic] # type = RandomIC # variable = temp # min = 922 # max = 1022 # [../] # [./group1_ic] # type = RandomIC # variable = group1 # min = .5 # max = 1.5 # [../] # [./group2_ic] # type = RandomIC # variable = group2 # min = .5 # max = 1.5 # [../] # [] 

The ICs block can be used to construct variable initial conditions. Documentation is here. The commented out ICs in this particular file are sometimes used to test the Jacobians of new kernels and boundary conditions introduced into Moltres.