## Example Input File

The input file example documented here is taken from moltres/tests/twod_axi_coupled/auto_diff_rho.i. This is a simple 2-D axisymmetric core model of the Molten Salt Reactor Experiment (MSRE) that was developed at Oak Ridge National Laboratory and was operated from 1965 through 1969. Simulation results from this 2-D model are documented in the article, Introduction to Moltres: An application for simulation of Molten Salt Reactors, which discusses simulation results, and compares them to a 3-D Moltres model of the MSRE and to MSRE data and calculated results. It should be noted that Figure 1 of the article indicates that the width of the model is 145 cm. This however, is the diameter of the entire core. A careful reader would notice that the width of the plots in the article is 1/2 this width, and the width indicated in Figure 1 is not representative of the model.

Assuming that Moltres has been successfully compiled, to execute this input file from the command line, run the following from a terminal window, substituting $moltres_root with the path to the Moltres root directory: cd$moltres_root/tests/twod_axi_coupled
../../moltres-opt -i auto_diff_rho.i


In serial, this job takes around 90 seconds on a 2.7 GHz machine. To run the job in parallel, execute:

mpirun -np 2 ../../moltres-opt -i auto_diff_rho.i


where the number of processors can be changed from 2 to however many processes you want to run. The parallel performance of the job depends on the number of degrees of freedom in the problem and the preconditioner used. A general rule of thumb for optimal scaling is not to go below 20k degrees of freedom per processor, otherwise communication becomes a performance drag. Additionally many preconditioners do not perform as well when spread over multiple processes as they lose access to “new” information. (See http://www.mcs.anl.gov/petsc/documentation/faq.html#slowerparallel for more discussion of this). This particular input file (auto_diff_rho.i) only has 8,697 degrees of freedom so communication is a factor; however, the executioner used is a direct solver which scales well. On the same 2.7 GHz machine, the solution times for 1-4 processors are given below.

• Single processor solution time: 90 seconds
• Two processors: 50 seconds
• Three: 35 seconds
• Four: 30 seconds

Before delving into a description of the input file, we note that all the parameter options for different input blocks can be seen by executing moltres-opt --dump.

Example output corresponding to the input file under discussion can be found in $moltres_root/tests/twod_axi_coupled/gold/auto_diff_rho.e. The most common application for visualizing output files is ParaView, although VisIt or yt may also be used. #### Model Geometry The figure below shows the domain for the 2-D MSRE model. It is a 72.5 cm by 151.75 cm rectangle that is slightly smaller than the total height of the core, and includes 1/2 the width of the core, extending from the core center line on the left to the core wall on the right. For this steady-state simulation, the core center line is a symmetry boundary. The domain consists of 14 fuel channels, alternating with 14 solid graphite moderator regions, represented in the figure by cyan and grey rectangles respectively. #### File Format Moltres is built on top of the MOOSE framework, and the input file uses the “hierarchal input text format” (hit) input format adopted by MOOSE. A brief description of the input syntax is presented here. This is a relatively simple file format that uses [names in brackets] to mark the start and end of input blocks. The format is loosely based on a directory structure with nesting of blocks allowed and [../] being used to indicate the end of a block (i.e., going up one level). Empty brackets [] can also be used to indicate the end of a block. Note that block names and parameter names are generally case sensitive in the input file. In addition, in Moltres/MOOSE input files, the # symbol is used to mark the start of a comment. Comments may start anywhere on a line. #### Substitution Variables Root level variables can be used as substitution variables throughout the document by using the syntax ${varname}. Starting at the top of the input file, the following substitution variables are defined:

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

• flow_velocity is used to set the upward flow velocity of the fuel / molten salt in this model.
• ini_temp is used below to set the initial temperature in the fuel and moderator.
• diri_temp is used to control the inlet temperature boundary condition.
• nt_scale is a transient fission heat source term scaling factor.

These variables may be modified to affect our primary system variables: temperature, neutron flux, and precursor concentrations. Decreasing the flow velocity will increase the temperature through the reactor. Because of the negative feedback coefficients of fuel and moderator for this reactor composition (modeled after Oak Ridge’s MSRE), the increase in average reactor temperature decreases the total reactor power and consequently the neutron fluxes and precursor concentrations. Similarly, increasing the inlet temperature via diri_temp decreases reactor power.

#### GlobalParams Block

Following the substitution variable 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 it is needed. Below is a description of the parameters included in the GlobalParams section:

• 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. Some of the kernel or boundary condition variables require an input named temperature which specifies the variable used to represent temperature. The variable temp will be specified below in the [Variables] block.
• 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

#### Variables Block

The Variables block is used to indicate the primary solution variables, or equivalently, to indicate the number of partial differential equations (PDEs) that will be defined in the Kernels and BCs blocks. For this model, the group1 and group2 neutron fluxes and the fuel and moderator temp (temperature) are the system variables that are being solved for by the PDEs. In the Kernels and BCs blocks described below, each kernel and BC term must be associated with one primary variable from the Variables list below to indicate which PDE the term is included in.

  [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 parameters purpose of the parameter is as follows: • family describes the shape function type used to form the approximate finite element solution. • order 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. #### Mesh Block Next in our input file we have the Mesh block. 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>. [Mesh] file = '2-D_lattice_structured.msh' []  Many MOOSE users generate their meshes using Cubit/Trelis. 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. #### Problem Block Next in our example input file, we have the Problem block. 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. [Problem] coord_type = RZ []  #### Precursors Block Whereas all the other blocks that have been introduced are standard MOOSE blocks, Precursors is a custom input file block unique to Moltres. The Precursors action sets up the delayed neutron precursor concentration equations: $\frac{\partial C_i}{\partial t} + \bar{u} \cdot \nabla C_i + \lambda_i C_i - \sum_{g'=1}^{G} \beta_i \nu \Sigma_{g'}^f \phi_{g'} = 0$ The precursor variables, kernels, and boundary conditions necessary for solving the precursor governing equations are all instantiated by the Precursors action. Six precursor groups (symbolized by the index i in the equation above) are modeled, as specified via the num_precursor_groups in the GlobalParams block. $$G$$ is the number of neutron flux energy groups, and $$g'$$ is the index associated with the energy groups. For this problem two energy groups are modeled, with the equations configured explicitly in the Kernels and BCs blocks documented after this section. [Precursors] [./pres] 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
[../]
[]


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 Block

The Kernels block is used to construct PDEs that are included in the system of equations that are solved. Each PDE has a primary variable that is being solved for, and the list of variables being solved for is defined in the Variables block shown above. There is an additional PDE solved as part of the system of PDEs for each variable defined in the Variables section. In this case, three solution variables were defined in the variable section:

• The group1 fast group neutron flux.
• The group2 thermal group neutron flux.
• The molten salt / moderator temperature (temp).

Note that additional precursor variables are automatically defined by the Precursors block.

The Kernels section defines a set of “Kernels”, where a “Kernel” represents a single term included in a PDE. A PDE is constructed by specifying the set of terms (or Kernels) that will be included in the PDE in the Kernels block, and by specifying which PDE the kernel is associated with. This is done by indicating which of the above three variables the kernel is associated with (i.e., group1, group2, or temp).

Thus each entry in the Kernels block specifies a term to include in one of PDEs that are solved. The type = <kernel type> parameter associated with a kernel entry identifies the term (or Kernel) that will be included in the PDE, and the variable = <primary variable> value indicates the primary solution variable (from the Variables block) associated with the term, or equivalently which PDE the term will be included in. MOOSE provides several standard kernels that can be included in a PDE. Moltres defines an additional set of kernels that are useful in modeling neutron flux and associated phenomenon in molten salt reactors. The mathematical form of the Moltres kernels can be found on the kernel wiki page.

Kernels can be optionally restricted to specific subdomains within the model by setting block = <subdomain_names>. Note that this implies that the form of the equation that is solved may differ in different mesh regions. The equations that are modeled are represented below, followed by the input required to construct these equations. In the group1 and group2 neutron flux equations below and in the input that follows, notice that the fission kernel (CoupledFissionKernel) is only included in the fuel region, and is not included in the moderator region (since there is no fuel in the moderator region). Also, the DelayedNeutronSource kernel, which contributes neutrons from the precursor group equations, is only included as part of the group1 or fast group equation.

In the heat transfer equation, the advection kernel (ConservativeTemperatureAdvection) is only included in the fuel region since advection is not relevant in the solid graphite moderator region. The fission heat source term is also restricted to the ‘Fuel’ region, since fission only occurs in the fuel region and not in the moderator region.

Neutronics Equation for group1 and group2 Variables (g = 1 or 2)

$\underbrace{\frac{1}{v_g}\frac{\partial \phi_g}{\partial t}}_{NtTimeDerivative} + \underbrace{\Sigma_g^r \phi_g}_{SigmaR} - \underbrace{\nabla \cdot D_g \nabla \phi_g}_{GroupDiffusion} - \underbrace{\sum_{g \ne g'}^G \Sigma_{g'\rightarrow g}^s \phi_{g'}}_{InScatter} - \underbrace{\chi_g^p \sum_{g' = 1}^G (1 - \beta) \nu \Sigma_{f,g'} \phi_{g'}}_{CoupledFissionKernel\\ \textrm{'Fuel' region only}} - \underbrace{\chi_g^d \sum_i^I \lambda_i C_i}_{DelayedNeutronSource\\ \textrm{'Fuel' region only} \\ \textrm{Not in group2 Eqn}} = 0$

Heat Transfer Equation for temp Variable

$\underbrace{\rho c_p \frac{\partial T}{\partial t}}_{[1]} + \underbrace{\rho c_p \bar{u} \cdot \nabla T}_{[2]~\textrm{'Fuel' region only}} - \underbrace{k \nabla^2 T}_{MatDiffusion \\ \textrm{(Conduction)}} - \underbrace{\sum_{g=1}^G \epsilon_{f,g}\Sigma_{f,g}\phi_g}_{TransientFissionHeatSource \\ \textrm{'Fuel' region only}} = 0$
• [1] = MatINSTemperatureTimeDerivative
• $$\bar{u}$$ = fuel / molten salt velocity
[Kernels]
#---------------------------------------------------------------------
# Group 1 Neutronics
#---------------------------------------------------------------------
[./time_group1]
type = NtTimeDerivative
variable = group1
group_number = 1
[../]
[./sigma_r_group1]
type = SigmaR
variable = group1
group_number = 1
[../]
[./diff_group1]
type = GroupDiffusion
variable = group1
group_number = 1
[../]
[./inscatter_group1]
type = InScatter
variable = group1
group_number = 1
[../]
[./fission_source_group1]
type = CoupledFissionKernel
variable = group1
group_number = 1
block = 'fuel'
[../]
[./delayed_group1]
type = DelayedNeutronSource
variable = group1
block = 'fuel'
[../]

#---------------------------------------------------------------------
# Group 2 Neutronics
#---------------------------------------------------------------------
[./time_group2]
type = NtTimeDerivative
variable = group2
group_number = 2
[../]
[./sigma_r_group2]
type = SigmaR
variable = group2
group_number = 2
[../]
[./diff_group2]
type = GroupDiffusion
variable = group2
group_number = 2
[../]
[./inscatter_group2]
type = InScatter
variable = group2
group_number = 2
[../]
[./fission_source_group2]
type = CoupledFissionKernel
variable = group2
group_number = 2
block = 'fuel'
[../]

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


#### BCs Block

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.

[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
[../]
boundary = 'fuel_tops'
type = TemperatureOutflowBC
variable = temp
velocity = '0 ${flow_velocity} 0' [../] []  #### Functions Block 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 substitution variable syntax ${<variable_name>}$ to access the values of ini_temp and diri_temp specified at the top of the input file. [Functions] [./temp_bc_func] type = ParsedFunction value = '${ini_temp} - (${ini_temp} -${diri_temp}) * tanh(t/1e-2)'
[../]
[]


#### Materials Block

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.

[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'
[../]
[]


Materials within the Materials block support the following parameters:

• property_tables_root: The path and prefix of the files that contain the macroscopic group constants that define neutron reaction rates. The suffix of these files identifies the property that each conveys. For example the file containing the fuel fission cross sections is in this example newt_msre_fuel_FISSXS.txt. Each of these files contains an interpolation table. The left column (column 1) is temperature. The remaining columns contain the macroscopic constants for different energy groups corresponding to the tabulated temperature, e.g. column 2 contains the constants for energy group 1, column 3 contains the constants for energy group 2, etc. The set of tables used in this example were generated with NEWT, part of the SCALE code system. Serpent, OpenMC, or any other macroscopic cross section generator may be used to create these simple input tables.
• 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.

Users can exert their greatest influence on the calculations through the Materials block. Increasing values of rho or cp will increase materials ability to store heat, enabling a greater reactor power. Because of application of an insulating boundary condition at the outer reactor wall in this example, modifying the thermal conductivity k has only a small impact on the simulation. However, if the conductivity is lowered by several orders of magnitude, the user will observe increases in radial gradients between the fuel channels and graphite as well as a decrease in reactor power. Use of different macroscopic group constant tables or direct modification of the current set would also influence simulation results.

#### Executioner and Preconditioning Blocks

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.

[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 -pc_factor_shift_type -pc_factor_shift_amount -ksp_type -snes_linesearch_minlambda'
petsc_options_value = 'lu       NONZERO               1e-10                   preonly   1e-3'
line_search = 'none'
# 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]
dt = 1e-3
cutback_factor = 0.4
growth_factor = 1.2
optimal_iterations = 20
[../]
[]

[Preconditioning]
[./SMP]
type = SMP
full = true
ksp_norm = none
[../]
[]


#### Postprocessors Block

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.

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


#### Outputs Block

Outputs documentation is here.

[Outputs]
print_perf_log = true
print_linear_residuals = true
[./exodus]
type = Exodus
file_base = 'auto_diff_rho'
execute_on = 'final'
[../]
[]


#### Debug Block

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

[Debug]
show_var_residual_norms = true
[]


#### ICs Block

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.

# [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
#   [../]
# []