alamo -------------------------- This is the main entry point for alamo and is a general-purpose launcher for many of the main integrators. Check the possible values for :code:`alamo.program` below to see the possible integrators that can be launched. .. raw:: html
Input name Description Value


Integrator::PhaseFieldMicrostructure<Model::Solid::Affine::Cubic>

Input name Description Value
pf.number_of_grains Number of grain fields (may be more if using different IC) 2
pf.M Mobility required
pf.gamma Phase field \(\gamma\) required
pf.sigma0 Initial GB energy if not using anisotropy required
pf.l_gb Mobility required
pf.elastic_df Determine whether to use elastic driving force false
pf.elastic_mult Multiplier of elastic energy 1.0
pf.threshold.value Value used for thresholding kinetic relation 0.0
pf.threshold.chempot Whether to include chemical potential in threshold false
pf.threshold.boundary Whether to include boundary energy in threshold false
pf.threshold.corner Whether to include corner regularization in threshold false
pf.threshold.lagrange Whether to include lagrange multiplier in threshold false
pf.threshold.mechanics Whether to include mechanical driving force in threshold false
pf.threshold.type Type of thresholding to use continuous chop
amr.max_level Maximum AMR level required
amr.ref_threshold Phase field refinement threshold 0.1
mechanics.type Reading this is redundant but necessary because of the way the code was originally structured (need to fix eventually) disable static dynamic
mechanics.tstart Elasticity 0.0
mechanics.mix_order Mixing order 1 2
mechanics.model_neuman_boundary Force Neumann BCs on the model false
mechanics.type Type of mecahnics to use. Static: do full implicit solve. Dynamic: evolve dynamic equations with explicit dynamics Disable: do nothing. disable static dynamic
mechanics.time_evolving Treat mechanics fields as changing in time. [false] You should use this if you care about other physics driven by the output of this integrator. false
mechanics.plot_disp Include displacement field in output true
mechanics.plot_rhs Include right-hand side in output true
mechanics.plot_psi Include \(\psi\) field in output true
mechanics.plot_stress Include stress in output true
mechanics.plot_strain Include strain in output true
mechanics.viscous.mu_dashpot Dashpot damping (damps velocity) 0.0
mechanics.viscous.mu_newton Newtonian viscous damping (damps velocity gradient) 0.0
mechanics.velocity.ic.type Initializer for RHS none expression
mechanics.bc.type Select the mechanical boundary conditions

mechanics.bc.constant.type.xloylozlo 3D Corner
mechanics.bc.constant.type.xloylozhi 3D Corner
mechanics.bc.constant.type.xloyhizlo 3D Corner
mechanics.bc.constant.type.xloyhizhi 3D Corner
mechanics.bc.constant.type.xhiylozlo 3D Corner
mechanics.bc.constant.type.xhiylozhi 3D Corner
mechanics.bc.constant.type.xhiyhizlo 3D Corner
mechanics.bc.constant.type.xhiyhizhi 3D Corner
mechanics.bc.constant.type.ylozlo 3D Edge
mechanics.bc.constant.type.ylozhi 3D Edge
mechanics.bc.constant.type.yhizlo 3D Edge
mechanics.bc.constant.type.yhizhi 3D Edge
mechanics.bc.constant.type.zloxlo 3D Edge
mechanics.bc.constant.type.zloxhi 3D Edge
mechanics.bc.constant.type.zhixlo 3D Edge
mechanics.bc.constant.type.zhixhi 3D Edge
mechanics.bc.constant.type.xloylo 3D Edge / 2D Corner
mechanics.bc.constant.type.xloyhi 3D Edge / 2D Corner
mechanics.bc.constant.type.xhiylo 3D Edge / 2D Corner
mechanics.bc.constant.type.xhiyhi 3D Edge / 2D Corner
mechanics.bc.constant.type.xlo 3D Face / 2D Edge
mechanics.bc.constant.type.xhi 3D Face / 2D Edge
mechanics.bc.constant.type.ylo 3D Face / 2D Edge
mechanics.bc.constant.type.yhi 3D Face / 2D Edge
mechanics.bc.constant.type.zlo 3D Face
mechanics.bc.constant.type.zhi 3D Face
mechanics.bc.constant.val.xloylozlo 3D Corner
mechanics.bc.constant.val.xloylozhi 3D Corner
mechanics.bc.constant.val.xloyhizlo 3D Corner
mechanics.bc.constant.val.xloyhizhi 3D Corner
mechanics.bc.constant.val.xhiylozlo 3D Corner
mechanics.bc.constant.val.xhiylozhi 3D Corner
mechanics.bc.constant.val.xhiyhizlo 3D Corner
mechanics.bc.constant.val.xhiyhizhi 3D Corner
mechanics.bc.constant.val.ylozlo 3D Edge
mechanics.bc.constant.val.ylozhi 3D Edge
mechanics.bc.constant.val.yhizlo 3D Edge
mechanics.bc.constant.val.yhizhi 3D Edge
mechanics.bc.constant.val.zloxlo 3D Edge
mechanics.bc.constant.val.zloxhi 3D Edge
mechanics.bc.constant.val.zhixlo 3D Edge
mechanics.bc.constant.val.zhixhi 3D Edge
mechanics.bc.constant.val.xloylo 3D Edge / 2D Corner
mechanics.bc.constant.val.xloyhi 3D Edge / 2D Corner
mechanics.bc.constant.val.xhiylo 3D Edge / 2D Corner
mechanics.bc.constant.val.xhiyhi 3D Edge / 2D Corner
mechanics.bc.constant.val.xlo 3D Face / 2D Edge
mechanics.bc.constant.val.xhi 3D Face / 2D Edge
mechanics.bc.constant.val.ylo 3D Face / 2D Edge
mechanics.bc.constant.val.yhi 3D Face / 2D Edge
mechanics.bc.constant.val.zlo 3D Face
mechanics.bc.constant.val.zhi 3D Face
mechanics.bc.tensiontest.type Tension test type. uniaxial_stress_clamp uniaxial_kolsky uniaxial_stress uniaxial_strain
mechanics.bc.tensiontest.disp Applied displacement (can be interpolator)
mechanics.bc.tensiontest.trac Applied traction (can be interpolator)
mechanics.print_model Print out model variables (if enabled by model) false
mechanics.rhs.type initial condition for right hand side (body force)

mechanics.rhs.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
mechanics.rhs.expression.coord coordinate system to use cartesian polar
mechanics.rhs.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
mechanics.rhs.trig.nr Number of real (cosin) waves
mechanics.rhs.trig.ni Number of imaginary (sin) waves
mechanics.rhs.trig.dim Spatial dimension
mechanics.rhs.trig.alpha Multiplier
mechanics.interval Timestep interval for elastic solves (default - solve every time) 0
mechanics.max_coarsening_level Maximum multigrid coarsening level (default - none, maximum coarsening) -1
mechanics.print_residual Whether to include residual output field false
mechanics.elastic_ref_threshold Whether to refine based on elastic solution 0.01
mechanics.zero_out_displacement Set this to true to zero out the displacement before each solve. (This is a temporary fix - we need to figure out why this is needed.) false
mechanics.tstart Time to start doing the elastic solve (by default, start immediately) -1.0
lagrange.on Lagrange multiplier method for enforcing volumes false
lagrange.lambda Lagrange multiplier value required
lagrange.vol0 Prescribed volume required
lagrange.tstart Lagrange multipler start time 0.0
sdf.on synthetic driving force (SDF) false
sdf.val value of SDF for each grain
sdf.tstart time to begin applying SDF 0.0
anisotropy.on Turn on false
anisotropy.beta Regularization para m required
anisotropy.tstart Time to turn on anisotropy required
anisotropy.timestep Modify timestep when turned on required
anisotropy.plot_int Modify plot_int when turned on -1
anisotropy.plot_dt Modify plot_dt when turned on -1.0
anisotropy.thermo_int Modify thermo int when turned on -1
anisotropy.thermo_plot_int Modify thermo plot int when turned on -1
anisotropy.elastic_int Frequency of elastic calculation -1
anisotropy.regularization Type of regularization to use k12 wilmore
anisotropy.type Type of GB to use

anisotropy.abssin.theta0 Angle offset (degrees)
anisotropy.abssin.sigma0 Minimum energy
anisotropy.abssin.sigma1 Energy multiplier
anisotropy.sin.theta0 Theta offset (degrees)
anisotropy.sin.sigma0 Minimum energy
anisotropy.sin.sigma1 Energy multiplier
anisotropy.sin.n Frequency number (integer)
anisotropy.read.filename Filename containing GB data file path
anisotropy.sh.theta0 Theta offset (degrees)
anisotropy.sh.phi0 Phi offset (radians)
anisotropy.sh.sigma0 Minimum energy value
anisotropy.sh.sigma1 Energy multiplier
anisotropy.sh.regularization Type of regularization to use: {wilhelm,k23}
fluctuation.on Thermal fluctuations
fluctuation.amp fluctuation amplitude
fluctuation.sd fluctuation stadard deviation
fluctuation.tstart time to start applying fluctuation
disconnection.on Disconnection generation
disconnection.tstart time to start applying disconnections 0.0
disconnection.nucleation_energy nucleation energy 0.0
disconnection.tau_vol characteristic time 1.0
disconnection.temp temperature 0.0
disconnection.box_size characteristic size 0.0
disconnection.interval interval between generation events required
disconnection.epsilon regularization epsilon 1E-20
disconnection.disconnection.fixed.on whether to manually specify disconnection nucleation points
disconnection.fixed.sitex array of x locations
disconnection.fixed.sitey array of y locations
disconnection.fixed.phases array of order parameter number
disconnection.fixed.time time to appear
disconnection.verbose verbosity false
shearcouple.on Shear coupling matrices false
bc.eta.type Boundary condition for eta

bc.eta.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
bc.eta.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
bc.eta.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
bc.eta.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
bc.eta.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.eta.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.eta.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
bc.eta.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
bc.eta.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
bc.eta.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
bc.eta.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
bc.eta.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0
ic.type Initial condition for the order parameter eta

ic.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
ic.perturbedinterface.wave_numbers Wave numbers
ic.perturbedinterface.wave_amplitudes Wave amplitudes
ic.perturbedinterface.normal Which axis is normal to the interface (x,y,z)
ic.perturbedinterface.offset Interface offset from origin
ic.perturbedinterface.reverse If true, flip the interface (default:false)
ic.perturbedinterface.mollifier Mollifier (options: dirac, [gaussian])
ic.perturbedinterface.eps Magnitude of mollifier
ic.voronoi.number_of_grains Number of grains
ic.voronoi.alpha Value to take in the region [1.0]
ic.voronoi.seed Random seed to use
ic.expression.coord coordinate system to use cartesian polar
ic.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
ic.sphere.radius Radius of the sphere 1.0
ic.sphere.center Vector location of the sphere center
ic.sphere.inside Value of the field inside the sphere 1.0
ic.sphere.outside Value of the field outside teh sphere 0.0
ic.sphere.type Type - can be cylinder oriented along the x, y, z directions or full sphere. xyz yz zx xy
ic.ellipse.x0 Coorinates of ellipse center
ic.ellipse.eps Diffuse boundary thickness 0.0
ic.ellipse.A DxD square matrix defining an ellipse.
ic.ellipse.a If A is not defined, then assume a sphere with radius a
ic.ellipse.number_of_inclusions Number of ellipses
ic.ellipse.center center of the ellipse
ic.ellipse.x0 center of the ellipse
ic.ellipse.A either a vector containing ellipse radii, or a matrix defining the ellipse
ic.ellipse.A Same
ic.ellipse.radius Array of radii [depricated]
ic.ellipse.eps Regularization for smooth boundary
ic.ellipse.invert Flip the inside and the outside
ic.random.offset offset from the [0,1] random number range 0.0
ic.random.mult multiplier for the [0,1] random number range 1.0
anisotropic_kinetics.on Anisotropic mobility 0
anisotropic_kinetics.tstart simulation time when anisotropic kinetics is activated 0.0
anisotropic_kinetics.mobility file containing anisotropic mobility data file path
anisotropic_kinetics.threshold file containing anisotropic mobility data file path


Integrator::PhaseFieldMicrostructure<Model::Solid::Affine::Hexagonal>

Input name Description Value
pf.number_of_grains Number of grain fields (may be more if using different IC) 2
pf.M Mobility required
pf.gamma Phase field \(\gamma\) required
pf.sigma0 Initial GB energy if not using anisotropy required
pf.l_gb Mobility required
pf.elastic_df Determine whether to use elastic driving force false
pf.elastic_mult Multiplier of elastic energy 1.0
pf.threshold.value Value used for thresholding kinetic relation 0.0
pf.threshold.chempot Whether to include chemical potential in threshold false
pf.threshold.boundary Whether to include boundary energy in threshold false
pf.threshold.corner Whether to include corner regularization in threshold false
pf.threshold.lagrange Whether to include lagrange multiplier in threshold false
pf.threshold.mechanics Whether to include mechanical driving force in threshold false
pf.threshold.type Type of thresholding to use continuous chop
amr.max_level Maximum AMR level required
amr.ref_threshold Phase field refinement threshold 0.1
mechanics.type Reading this is redundant but necessary because of the way the code was originally structured (need to fix eventually) disable static dynamic
mechanics.tstart Elasticity 0.0
mechanics.mix_order Mixing order 1 2
mechanics.model_neuman_boundary Force Neumann BCs on the model false
mechanics.type Type of mecahnics to use. Static: do full implicit solve. Dynamic: evolve dynamic equations with explicit dynamics Disable: do nothing. disable static dynamic
mechanics.time_evolving Treat mechanics fields as changing in time. [false] You should use this if you care about other physics driven by the output of this integrator. false
mechanics.plot_disp Include displacement field in output true
mechanics.plot_rhs Include right-hand side in output true
mechanics.plot_psi Include \(\psi\) field in output true
mechanics.plot_stress Include stress in output true
mechanics.plot_strain Include strain in output true
mechanics.viscous.mu_dashpot Dashpot damping (damps velocity) 0.0
mechanics.viscous.mu_newton Newtonian viscous damping (damps velocity gradient) 0.0
mechanics.velocity.ic.type Initializer for RHS none expression
mechanics.bc.type Select the mechanical boundary conditions

mechanics.bc.constant.type.xloylozlo 3D Corner
mechanics.bc.constant.type.xloylozhi 3D Corner
mechanics.bc.constant.type.xloyhizlo 3D Corner
mechanics.bc.constant.type.xloyhizhi 3D Corner
mechanics.bc.constant.type.xhiylozlo 3D Corner
mechanics.bc.constant.type.xhiylozhi 3D Corner
mechanics.bc.constant.type.xhiyhizlo 3D Corner
mechanics.bc.constant.type.xhiyhizhi 3D Corner
mechanics.bc.constant.type.ylozlo 3D Edge
mechanics.bc.constant.type.ylozhi 3D Edge
mechanics.bc.constant.type.yhizlo 3D Edge
mechanics.bc.constant.type.yhizhi 3D Edge
mechanics.bc.constant.type.zloxlo 3D Edge
mechanics.bc.constant.type.zloxhi 3D Edge
mechanics.bc.constant.type.zhixlo 3D Edge
mechanics.bc.constant.type.zhixhi 3D Edge
mechanics.bc.constant.type.xloylo 3D Edge / 2D Corner
mechanics.bc.constant.type.xloyhi 3D Edge / 2D Corner
mechanics.bc.constant.type.xhiylo 3D Edge / 2D Corner
mechanics.bc.constant.type.xhiyhi 3D Edge / 2D Corner
mechanics.bc.constant.type.xlo 3D Face / 2D Edge
mechanics.bc.constant.type.xhi 3D Face / 2D Edge
mechanics.bc.constant.type.ylo 3D Face / 2D Edge
mechanics.bc.constant.type.yhi 3D Face / 2D Edge
mechanics.bc.constant.type.zlo 3D Face
mechanics.bc.constant.type.zhi 3D Face
mechanics.bc.constant.val.xloylozlo 3D Corner
mechanics.bc.constant.val.xloylozhi 3D Corner
mechanics.bc.constant.val.xloyhizlo 3D Corner
mechanics.bc.constant.val.xloyhizhi 3D Corner
mechanics.bc.constant.val.xhiylozlo 3D Corner
mechanics.bc.constant.val.xhiylozhi 3D Corner
mechanics.bc.constant.val.xhiyhizlo 3D Corner
mechanics.bc.constant.val.xhiyhizhi 3D Corner
mechanics.bc.constant.val.ylozlo 3D Edge
mechanics.bc.constant.val.ylozhi 3D Edge
mechanics.bc.constant.val.yhizlo 3D Edge
mechanics.bc.constant.val.yhizhi 3D Edge
mechanics.bc.constant.val.zloxlo 3D Edge
mechanics.bc.constant.val.zloxhi 3D Edge
mechanics.bc.constant.val.zhixlo 3D Edge
mechanics.bc.constant.val.zhixhi 3D Edge
mechanics.bc.constant.val.xloylo 3D Edge / 2D Corner
mechanics.bc.constant.val.xloyhi 3D Edge / 2D Corner
mechanics.bc.constant.val.xhiylo 3D Edge / 2D Corner
mechanics.bc.constant.val.xhiyhi 3D Edge / 2D Corner
mechanics.bc.constant.val.xlo 3D Face / 2D Edge
mechanics.bc.constant.val.xhi 3D Face / 2D Edge
mechanics.bc.constant.val.ylo 3D Face / 2D Edge
mechanics.bc.constant.val.yhi 3D Face / 2D Edge
mechanics.bc.constant.val.zlo 3D Face
mechanics.bc.constant.val.zhi 3D Face
mechanics.bc.tensiontest.type Tension test type. uniaxial_stress_clamp uniaxial_kolsky uniaxial_stress uniaxial_strain
mechanics.bc.tensiontest.disp Applied displacement (can be interpolator)
mechanics.bc.tensiontest.trac Applied traction (can be interpolator)
mechanics.print_model Print out model variables (if enabled by model) false
mechanics.rhs.type initial condition for right hand side (body force)

mechanics.rhs.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
mechanics.rhs.expression.coord coordinate system to use cartesian polar
mechanics.rhs.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
mechanics.rhs.trig.nr Number of real (cosin) waves
mechanics.rhs.trig.ni Number of imaginary (sin) waves
mechanics.rhs.trig.dim Spatial dimension
mechanics.rhs.trig.alpha Multiplier
mechanics.interval Timestep interval for elastic solves (default - solve every time) 0
mechanics.max_coarsening_level Maximum multigrid coarsening level (default - none, maximum coarsening) -1
mechanics.print_residual Whether to include residual output field false
mechanics.elastic_ref_threshold Whether to refine based on elastic solution 0.01
mechanics.zero_out_displacement Set this to true to zero out the displacement before each solve. (This is a temporary fix - we need to figure out why this is needed.) false
mechanics.tstart Time to start doing the elastic solve (by default, start immediately) -1.0
lagrange.on Lagrange multiplier method for enforcing volumes false
lagrange.lambda Lagrange multiplier value required
lagrange.vol0 Prescribed volume required
lagrange.tstart Lagrange multipler start time 0.0
sdf.on synthetic driving force (SDF) false
sdf.val value of SDF for each grain
sdf.tstart time to begin applying SDF 0.0
anisotropy.on Turn on false
anisotropy.beta Regularization para m required
anisotropy.tstart Time to turn on anisotropy required
anisotropy.timestep Modify timestep when turned on required
anisotropy.plot_int Modify plot_int when turned on -1
anisotropy.plot_dt Modify plot_dt when turned on -1.0
anisotropy.thermo_int Modify thermo int when turned on -1
anisotropy.thermo_plot_int Modify thermo plot int when turned on -1
anisotropy.elastic_int Frequency of elastic calculation -1
anisotropy.regularization Type of regularization to use k12 wilmore
anisotropy.type Type of GB to use

anisotropy.abssin.theta0 Angle offset (degrees)
anisotropy.abssin.sigma0 Minimum energy
anisotropy.abssin.sigma1 Energy multiplier
anisotropy.sin.theta0 Theta offset (degrees)
anisotropy.sin.sigma0 Minimum energy
anisotropy.sin.sigma1 Energy multiplier
anisotropy.sin.n Frequency number (integer)
anisotropy.read.filename Filename containing GB data file path
anisotropy.sh.theta0 Theta offset (degrees)
anisotropy.sh.phi0 Phi offset (radians)
anisotropy.sh.sigma0 Minimum energy value
anisotropy.sh.sigma1 Energy multiplier
anisotropy.sh.regularization Type of regularization to use: {wilhelm,k23}
fluctuation.on Thermal fluctuations
fluctuation.amp fluctuation amplitude
fluctuation.sd fluctuation stadard deviation
fluctuation.tstart time to start applying fluctuation
disconnection.on Disconnection generation
disconnection.tstart time to start applying disconnections 0.0
disconnection.nucleation_energy nucleation energy 0.0
disconnection.tau_vol characteristic time 1.0
disconnection.temp temperature 0.0
disconnection.box_size characteristic size 0.0
disconnection.interval interval between generation events required
disconnection.epsilon regularization epsilon 1E-20
disconnection.disconnection.fixed.on whether to manually specify disconnection nucleation points
disconnection.fixed.sitex array of x locations
disconnection.fixed.sitey array of y locations
disconnection.fixed.phases array of order parameter number
disconnection.fixed.time time to appear
disconnection.verbose verbosity false
shearcouple.on Shear coupling matrices false
bc.eta.type Boundary condition for eta

bc.eta.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
bc.eta.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
bc.eta.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
bc.eta.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
bc.eta.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.eta.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.eta.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
bc.eta.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
bc.eta.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
bc.eta.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
bc.eta.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
bc.eta.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0
ic.type Initial condition for the order parameter eta

ic.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
ic.perturbedinterface.wave_numbers Wave numbers
ic.perturbedinterface.wave_amplitudes Wave amplitudes
ic.perturbedinterface.normal Which axis is normal to the interface (x,y,z)
ic.perturbedinterface.offset Interface offset from origin
ic.perturbedinterface.reverse If true, flip the interface (default:false)
ic.perturbedinterface.mollifier Mollifier (options: dirac, [gaussian])
ic.perturbedinterface.eps Magnitude of mollifier
ic.voronoi.number_of_grains Number of grains
ic.voronoi.alpha Value to take in the region [1.0]
ic.voronoi.seed Random seed to use
ic.expression.coord coordinate system to use cartesian polar
ic.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
ic.sphere.radius Radius of the sphere 1.0
ic.sphere.center Vector location of the sphere center
ic.sphere.inside Value of the field inside the sphere 1.0
ic.sphere.outside Value of the field outside teh sphere 0.0
ic.sphere.type Type - can be cylinder oriented along the x, y, z directions or full sphere. xyz yz zx xy
ic.ellipse.x0 Coorinates of ellipse center
ic.ellipse.eps Diffuse boundary thickness 0.0
ic.ellipse.A DxD square matrix defining an ellipse.
ic.ellipse.a If A is not defined, then assume a sphere with radius a
ic.ellipse.number_of_inclusions Number of ellipses
ic.ellipse.center center of the ellipse
ic.ellipse.x0 center of the ellipse
ic.ellipse.A either a vector containing ellipse radii, or a matrix defining the ellipse
ic.ellipse.A Same
ic.ellipse.radius Array of radii [depricated]
ic.ellipse.eps Regularization for smooth boundary
ic.ellipse.invert Flip the inside and the outside
ic.random.offset offset from the [0,1] random number range 0.0
ic.random.mult multiplier for the [0,1] random number range 1.0
anisotropic_kinetics.on Anisotropic mobility 0
anisotropic_kinetics.tstart simulation time when anisotropic kinetics is activated 0.0
anisotropic_kinetics.mobility file containing anisotropic mobility data file path
anisotropic_kinetics.threshold file containing anisotropic mobility data file path


Integrator::PhaseFieldMicrostructure<Model::Solid::Finite::PseudoAffine::Cubic>

Input name Description Value
pf.number_of_grains Number of grain fields (may be more if using different IC) 2
pf.M Mobility required
pf.gamma Phase field \(\gamma\) required
pf.sigma0 Initial GB energy if not using anisotropy required
pf.l_gb Mobility required
pf.elastic_df Determine whether to use elastic driving force false
pf.elastic_mult Multiplier of elastic energy 1.0
pf.threshold.value Value used for thresholding kinetic relation 0.0
pf.threshold.chempot Whether to include chemical potential in threshold false
pf.threshold.boundary Whether to include boundary energy in threshold false
pf.threshold.corner Whether to include corner regularization in threshold false
pf.threshold.lagrange Whether to include lagrange multiplier in threshold false
pf.threshold.mechanics Whether to include mechanical driving force in threshold false
pf.threshold.type Type of thresholding to use continuous chop
amr.max_level Maximum AMR level required
amr.ref_threshold Phase field refinement threshold 0.1
mechanics.type Reading this is redundant but necessary because of the way the code was originally structured (need to fix eventually) disable static dynamic
mechanics.tstart Elasticity 0.0
mechanics.mix_order Mixing order 1 2
mechanics.model_neuman_boundary Force Neumann BCs on the model false
mechanics.type Type of mecahnics to use. Static: do full implicit solve. Dynamic: evolve dynamic equations with explicit dynamics Disable: do nothing. disable static dynamic
mechanics.time_evolving Treat mechanics fields as changing in time. [false] You should use this if you care about other physics driven by the output of this integrator. false
mechanics.plot_disp Include displacement field in output true
mechanics.plot_rhs Include right-hand side in output true
mechanics.plot_psi Include \(\psi\) field in output true
mechanics.plot_stress Include stress in output true
mechanics.plot_strain Include strain in output true
mechanics.viscous.mu_dashpot Dashpot damping (damps velocity) 0.0
mechanics.viscous.mu_newton Newtonian viscous damping (damps velocity gradient) 0.0
mechanics.velocity.ic.type Initializer for RHS none expression
mechanics.bc.type Select the mechanical boundary conditions

mechanics.bc.constant.type.xloylozlo 3D Corner
mechanics.bc.constant.type.xloylozhi 3D Corner
mechanics.bc.constant.type.xloyhizlo 3D Corner
mechanics.bc.constant.type.xloyhizhi 3D Corner
mechanics.bc.constant.type.xhiylozlo 3D Corner
mechanics.bc.constant.type.xhiylozhi 3D Corner
mechanics.bc.constant.type.xhiyhizlo 3D Corner
mechanics.bc.constant.type.xhiyhizhi 3D Corner
mechanics.bc.constant.type.ylozlo 3D Edge
mechanics.bc.constant.type.ylozhi 3D Edge
mechanics.bc.constant.type.yhizlo 3D Edge
mechanics.bc.constant.type.yhizhi 3D Edge
mechanics.bc.constant.type.zloxlo 3D Edge
mechanics.bc.constant.type.zloxhi 3D Edge
mechanics.bc.constant.type.zhixlo 3D Edge
mechanics.bc.constant.type.zhixhi 3D Edge
mechanics.bc.constant.type.xloylo 3D Edge / 2D Corner
mechanics.bc.constant.type.xloyhi 3D Edge / 2D Corner
mechanics.bc.constant.type.xhiylo 3D Edge / 2D Corner
mechanics.bc.constant.type.xhiyhi 3D Edge / 2D Corner
mechanics.bc.constant.type.xlo 3D Face / 2D Edge
mechanics.bc.constant.type.xhi 3D Face / 2D Edge
mechanics.bc.constant.type.ylo 3D Face / 2D Edge
mechanics.bc.constant.type.yhi 3D Face / 2D Edge
mechanics.bc.constant.type.zlo 3D Face
mechanics.bc.constant.type.zhi 3D Face
mechanics.bc.constant.val.xloylozlo 3D Corner
mechanics.bc.constant.val.xloylozhi 3D Corner
mechanics.bc.constant.val.xloyhizlo 3D Corner
mechanics.bc.constant.val.xloyhizhi 3D Corner
mechanics.bc.constant.val.xhiylozlo 3D Corner
mechanics.bc.constant.val.xhiylozhi 3D Corner
mechanics.bc.constant.val.xhiyhizlo 3D Corner
mechanics.bc.constant.val.xhiyhizhi 3D Corner
mechanics.bc.constant.val.ylozlo 3D Edge
mechanics.bc.constant.val.ylozhi 3D Edge
mechanics.bc.constant.val.yhizlo 3D Edge
mechanics.bc.constant.val.yhizhi 3D Edge
mechanics.bc.constant.val.zloxlo 3D Edge
mechanics.bc.constant.val.zloxhi 3D Edge
mechanics.bc.constant.val.zhixlo 3D Edge
mechanics.bc.constant.val.zhixhi 3D Edge
mechanics.bc.constant.val.xloylo 3D Edge / 2D Corner
mechanics.bc.constant.val.xloyhi 3D Edge / 2D Corner
mechanics.bc.constant.val.xhiylo 3D Edge / 2D Corner
mechanics.bc.constant.val.xhiyhi 3D Edge / 2D Corner
mechanics.bc.constant.val.xlo 3D Face / 2D Edge
mechanics.bc.constant.val.xhi 3D Face / 2D Edge
mechanics.bc.constant.val.ylo 3D Face / 2D Edge
mechanics.bc.constant.val.yhi 3D Face / 2D Edge
mechanics.bc.constant.val.zlo 3D Face
mechanics.bc.constant.val.zhi 3D Face
mechanics.bc.tensiontest.type Tension test type. uniaxial_stress_clamp uniaxial_kolsky uniaxial_stress uniaxial_strain
mechanics.bc.tensiontest.disp Applied displacement (can be interpolator)
mechanics.bc.tensiontest.trac Applied traction (can be interpolator)
mechanics.print_model Print out model variables (if enabled by model) false
mechanics.rhs.type initial condition for right hand side (body force)

mechanics.rhs.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
mechanics.rhs.expression.coord coordinate system to use cartesian polar
mechanics.rhs.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
mechanics.rhs.trig.nr Number of real (cosin) waves
mechanics.rhs.trig.ni Number of imaginary (sin) waves
mechanics.rhs.trig.dim Spatial dimension
mechanics.rhs.trig.alpha Multiplier
mechanics.interval Timestep interval for elastic solves (default - solve every time) 0
mechanics.max_coarsening_level Maximum multigrid coarsening level (default - none, maximum coarsening) -1
mechanics.print_residual Whether to include residual output field false
mechanics.elastic_ref_threshold Whether to refine based on elastic solution 0.01
mechanics.zero_out_displacement Set this to true to zero out the displacement before each solve. (This is a temporary fix - we need to figure out why this is needed.) false
mechanics.tstart Time to start doing the elastic solve (by default, start immediately) -1.0
lagrange.on Lagrange multiplier method for enforcing volumes false
lagrange.lambda Lagrange multiplier value required
lagrange.vol0 Prescribed volume required
lagrange.tstart Lagrange multipler start time 0.0
sdf.on synthetic driving force (SDF) false
sdf.val value of SDF for each grain
sdf.tstart time to begin applying SDF 0.0
anisotropy.on Turn on false
anisotropy.beta Regularization para m required
anisotropy.tstart Time to turn on anisotropy required
anisotropy.timestep Modify timestep when turned on required
anisotropy.plot_int Modify plot_int when turned on -1
anisotropy.plot_dt Modify plot_dt when turned on -1.0
anisotropy.thermo_int Modify thermo int when turned on -1
anisotropy.thermo_plot_int Modify thermo plot int when turned on -1
anisotropy.elastic_int Frequency of elastic calculation -1
anisotropy.regularization Type of regularization to use k12 wilmore
anisotropy.type Type of GB to use

anisotropy.abssin.theta0 Angle offset (degrees)
anisotropy.abssin.sigma0 Minimum energy
anisotropy.abssin.sigma1 Energy multiplier
anisotropy.sin.theta0 Theta offset (degrees)
anisotropy.sin.sigma0 Minimum energy
anisotropy.sin.sigma1 Energy multiplier
anisotropy.sin.n Frequency number (integer)
anisotropy.read.filename Filename containing GB data file path
anisotropy.sh.theta0 Theta offset (degrees)
anisotropy.sh.phi0 Phi offset (radians)
anisotropy.sh.sigma0 Minimum energy value
anisotropy.sh.sigma1 Energy multiplier
anisotropy.sh.regularization Type of regularization to use: {wilhelm,k23}
fluctuation.on Thermal fluctuations
fluctuation.amp fluctuation amplitude
fluctuation.sd fluctuation stadard deviation
fluctuation.tstart time to start applying fluctuation
disconnection.on Disconnection generation
disconnection.tstart time to start applying disconnections 0.0
disconnection.nucleation_energy nucleation energy 0.0
disconnection.tau_vol characteristic time 1.0
disconnection.temp temperature 0.0
disconnection.box_size characteristic size 0.0
disconnection.interval interval between generation events required
disconnection.epsilon regularization epsilon 1E-20
disconnection.disconnection.fixed.on whether to manually specify disconnection nucleation points
disconnection.fixed.sitex array of x locations
disconnection.fixed.sitey array of y locations
disconnection.fixed.phases array of order parameter number
disconnection.fixed.time time to appear
disconnection.verbose verbosity false
shearcouple.on Shear coupling matrices false
bc.eta.type Boundary condition for eta

bc.eta.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
bc.eta.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
bc.eta.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
bc.eta.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
bc.eta.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.eta.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.eta.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
bc.eta.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
bc.eta.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
bc.eta.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
bc.eta.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
bc.eta.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0
ic.type Initial condition for the order parameter eta

ic.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
ic.perturbedinterface.wave_numbers Wave numbers
ic.perturbedinterface.wave_amplitudes Wave amplitudes
ic.perturbedinterface.normal Which axis is normal to the interface (x,y,z)
ic.perturbedinterface.offset Interface offset from origin
ic.perturbedinterface.reverse If true, flip the interface (default:false)
ic.perturbedinterface.mollifier Mollifier (options: dirac, [gaussian])
ic.perturbedinterface.eps Magnitude of mollifier
ic.voronoi.number_of_grains Number of grains
ic.voronoi.alpha Value to take in the region [1.0]
ic.voronoi.seed Random seed to use
ic.expression.coord coordinate system to use cartesian polar
ic.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
ic.sphere.radius Radius of the sphere 1.0
ic.sphere.center Vector location of the sphere center
ic.sphere.inside Value of the field inside the sphere 1.0
ic.sphere.outside Value of the field outside teh sphere 0.0
ic.sphere.type Type - can be cylinder oriented along the x, y, z directions or full sphere. xyz yz zx xy
ic.ellipse.x0 Coorinates of ellipse center
ic.ellipse.eps Diffuse boundary thickness 0.0
ic.ellipse.A DxD square matrix defining an ellipse.
ic.ellipse.a If A is not defined, then assume a sphere with radius a
ic.ellipse.number_of_inclusions Number of ellipses
ic.ellipse.center center of the ellipse
ic.ellipse.x0 center of the ellipse
ic.ellipse.A either a vector containing ellipse radii, or a matrix defining the ellipse
ic.ellipse.A Same
ic.ellipse.radius Array of radii [depricated]
ic.ellipse.eps Regularization for smooth boundary
ic.ellipse.invert Flip the inside and the outside
ic.random.offset offset from the [0,1] random number range 0.0
ic.random.mult multiplier for the [0,1] random number range 1.0
anisotropic_kinetics.on Anisotropic mobility 0
anisotropic_kinetics.tstart simulation time when anisotropic kinetics is activated 0.0
anisotropic_kinetics.mobility file containing anisotropic mobility data file path
anisotropic_kinetics.threshold file containing anisotropic mobility data file path


Integrator::Flame

Input name Description Value
plot_field Whether to include extra fields (such as mdot, etc) in the plot output true
timestep Simulation timestep 1.0e-4
pf.eps Burn width thickness 0.0
pf.kappa Interface energy param 0.0
pf.gamma Scaling factor for mobility 1.0
pf.lambda Chemical potential multiplier 0.0
pf.w1 Unburned rest energy 0.0
pf.w12 Barrier energy 0.0
pf.w0 Burned rest energy 0.0
amr.ghost_cells number of ghost cells in all fields 2
geometry.x_len Domain x length 0.001
geometry.y_len Domain y length 0.001
pf.eta.bc.type Boundary conditions for phase field order params

pf.eta.bc.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
pf.eta.bc.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
pf.eta.bc.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
pf.eta.bc.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
pf.eta.bc.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
pf.eta.bc.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
pf.eta.bc.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
pf.eta.bc.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
pf.eta.bc.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
pf.eta.bc.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
pf.eta.bc.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
pf.eta.bc.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0
pf.eta.ic.type phase field initial condition

pf.eta.ic.laminate.number_of_inclusions How many laminates (MUST be greater than or equal to 1). 1
pf.eta.ic.laminate.orientation Vector normal to the interface of the laminate
pf.eta.ic.laminate.eps Diffuse thickness
pf.eta.ic.laminate.mollifier Type of mollifer to use (options: dirac, [gaussian])
pf.eta.ic.laminate.singlefab Switch to mode where only one component is used.
pf.eta.ic.laminate.invert Take the complement of the laminate
pf.eta.ic.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
pf.eta.ic.expression.coord coordinate system to use cartesian polar
pf.eta.ic.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
pf.eta.ic.bmp.filename BMP filename. file path
pf.eta.ic.bmp.fit How to position image in space stretch fitheight fitwidth coord
pf.eta.ic.bmp.coord.lo Location of lower-left corner in the domain
pf.eta.ic.bmp.coord.hi Location of upper-right corner in the domain
pf.eta.ic.bmp.channel Color channel to use r g b R G B
pf.eta.ic.bmp.min Scaling value - minimum 0.0
pf.eta.ic.bmp.max Scaling value - maximum 255.0
pf.eta.ic.png.channel Color channel to use (options: r, R, g, G, b, B, a, A) r g b a R G B A
pf.eta.ic.png.filename BMP filename. file path
pf.eta.ic.png.fit how to position the image stretch fitheight fitwidth coord
pf.eta.ic.png.coord.lo Lower-left coordinates of image in domain
pf.eta.ic.png.coord.hi Upper-right coordinates of image in domain
pf.eta.ic.png.min Desired minimum value to scale pixels by 0.0
pf.eta.ic.png.max Desired maximum value to scale pixels by 255.0
thermal.on IO::ParmParse pp("thermal"); Whether to use the Thermal Transport Model false
elastic.on Whether to use Neo-hookean Elastic model 0
thermal.bound System Initial Temperature 0.0
elastic.traction Body force 0.0
elastic.phirefinement Phi refinement criteria 1
thermal.rho_ap AP Density required
thermal.rho_htpb HTPB Density required
thermal.k_ap AP Thermal Conductivity required
thermal.k_htpb HTPB Thermal Conductivity required
thermal.cp_ap AP Specific Heat required
thermal.cp_htpb HTPB Specific Heat required
thermal.q0 Baseline heat flux 0.0
thermal.m_ap AP Pre-exponential factor for Arrhenius Law required
thermal.m_htpb HTPB Pre-exponential factor for Arrhenius Law required
thermal.E_ap AP Activation Energy for Arrhenius Law required
thermal.E_htpb HTPB Activation Energy for Arrhenius Law required
thermal.hc Used to change heat flux units 1.0
thermal.massfraction Systen AP mass fraction 0.8
thermal.mlocal_ap AP mass flux reference value 0.0
thermal.mlocal_htpb HTPB mass flux reference value 0.0
thermal.mlocal_comb AP/HTPB mass flux reference value 0.0
thermal.T_fluid Temperature of the Standin Fluid 300.0
thermal.disperssion1 K; dispersion variables are use to set the outter field properties for the void grain case.
thermal.disperssion2 rho; dispersion variables are use to set the outter field properties for the void grain case.
thermal.disperssion3 cp; dispersion variables are use to set the outter field properties for the void grain case.
thermal.modeling_ap Scaling factor for AP thermal conductivity (default = 1.0) 1.0
thermal.modeling_htpb Scaling factor for HTPB thermal conductivity (default = 1.0) 1.0
thermal.temp.bc.type Temperature boundary condition

thermal.temp.bc.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
thermal.temp.bc.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
thermal.temp.bc.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
thermal.temp.bc.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
thermal.temp.bc.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
thermal.temp.bc.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
thermal.temp.bc.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
thermal.temp.bc.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
thermal.temp.bc.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
thermal.temp.bc.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
thermal.temp.bc.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
thermal.temp.bc.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0
laser.ic.type laser initial condition

laser.ic.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
laser.ic.expression.coord coordinate system to use cartesian polar
laser.ic.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
temp.ic.type thermal initial condition

temp.ic.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
temp.ic.expression.coord coordinate system to use cartesian polar
temp.ic.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
temp.ic.bmp.filename BMP filename. file path
temp.ic.bmp.fit How to position image in space stretch fitheight fitwidth coord
temp.ic.bmp.coord.lo Location of lower-left corner in the domain
temp.ic.bmp.coord.hi Location of upper-right corner in the domain
temp.ic.bmp.channel Color channel to use r g b R G B
temp.ic.bmp.min Scaling value - minimum 0.0
temp.ic.bmp.max Scaling value - maximum 255.0
temp.ic.png.channel Color channel to use (options: r, R, g, G, b, B, a, A) r g b a R G B A
temp.ic.png.filename BMP filename. file path
temp.ic.png.fit how to position the image stretch fitheight fitwidth coord
temp.ic.png.coord.lo Lower-left coordinates of image in domain
temp.ic.png.coord.hi Upper-right coordinates of image in domain
temp.ic.png.min Desired minimum value to scale pixels by 0.0
temp.ic.png.max Desired maximum value to scale pixels by 255.0
pressure.P Constant pressure value 1.0
pressure.a1 Surgate heat flux model paramater - AP required
pressure.a2 Surgate heat flux model paramater - HTPB required
pressure.a3 Surgate heat flux model paramater - Total required
pressure.b1 Surgate heat flux model paramater - AP required
pressure.b2 Surgate heat flux model paramater - HTPB required
pressure.b3 Surgate heat flux model paramater - Total required
pressure.c1 Surgate heat flux model paramater - Total required
pressure.mob_ap Whether to include pressure to the arrhenius law 0
pressure.dependency Whether to use pressure to determined the reference Zeta 1
pressure.h1 Surgate heat flux model paramater - Homogenized 1.81
pressure.h2 Surgate heat flux model paramater - Homogenized 1.34
pressure.r_ap AP power pressure law parameter (r*P^n) required
pressure.r_htpb HTPB power pressure law parameter (r*P^n) required
pressure.r_comb AP/HTPB power pressure law parameter (r*P^n) required
pressure.n_ap AP power pressure law parameter (r*P^n) required
pressure.n_htpb HTPB power pressure law parameter (r*P^n) required
pressure.n_comb AP/HTPB power pressure law parameter (r*P^n) required
variable_pressure Whether to compute the pressure evolution 0
homogeneousSystem Whether to initialize Phi with homogenized properties 0
amr.refinement_criterion Refinement criterion for eta field 0.001
amr.refinement_criterion_temp Refinement criterion for temperature field 0.001
amr.refinament_restriction Eta value to restrict the refinament for the temperature field 0.1
amr.phi_refinement_criterion Refinement criterion for phi field [infinity] 1.0e100
small Lowest value of Eta. 1.0e-8
phi.ic.type IC type (psread, laminate, constant) psread laminate expression constant bmp png
phi.ic.psread.eps value.ic_phicell = new IC::PSRead(value.geom, pp, "phi.ic.psread"); AP/HTPB interface length 1.0e-5
phi.zeta_0 Reference interface length for heat integration 1.0e-5
phi.ic.laminate.eps value.ic_phicell = new IC::Laminate(value.geom, pp, "phi.ic.laminate"); AP/HTPB interface length 1.0e-5
phi.zeta_0 Reference interface length for heat integration 1.0e-5
phi.zeta_0 value.ic_phicell = new IC::Expression(value.geom, pp, "phi.ic.expression"); Reference interface length for heat integration 1.0e-5
phi.zeta AP/HTPB interface length 1.0e-5
phi.zeta_0 value.ic_phicell = new IC::Constant(value.geom, pp, "phi.ic.constant"); Reference interface length for heat integration 1.0e-5
phi.zeta AP/HTPB interface length 1.0e-5
phi.zeta_0 value.ic_phicell = new IC::BMP(value.geom, pp, "phi.ic.bmp"); Reference interface length for heat integration 1.0e-5
phi.zeta AP/HTPB interface length 1.0e-5
phi.zeta_0 Reference interface length for heat integration 1.0e-5
phi.zeta AP/HTPB interface length 1.0e-5
elastic.type Type of mecahnics to use. Static: do full implicit solve. Dynamic: evolve dynamic equations with explicit dynamics Disable: do nothing. disable static dynamic
elastic.time_evolving Treat mechanics fields as changing in time. [false] You should use this if you care about other physics driven by the output of this integrator. false
elastic.plot_disp Include displacement field in output true
elastic.plot_rhs Include right-hand side in output true
elastic.plot_psi Include \(\psi\) field in output true
elastic.plot_stress Include stress in output true
elastic.plot_strain Include strain in output true
elastic.viscous.mu_dashpot Dashpot damping (damps velocity) 0.0
elastic.viscous.mu_newton Newtonian viscous damping (damps velocity gradient) 0.0
elastic.velocity.ic.type Initializer for RHS none expression
elastic.bc.type Select the mechanical boundary conditions

elastic.bc.constant.type.xloylozlo 3D Corner
elastic.bc.constant.type.xloylozhi 3D Corner
elastic.bc.constant.type.xloyhizlo 3D Corner
elastic.bc.constant.type.xloyhizhi 3D Corner
elastic.bc.constant.type.xhiylozlo 3D Corner
elastic.bc.constant.type.xhiylozhi 3D Corner
elastic.bc.constant.type.xhiyhizlo 3D Corner
elastic.bc.constant.type.xhiyhizhi 3D Corner
elastic.bc.constant.type.ylozlo 3D Edge
elastic.bc.constant.type.ylozhi 3D Edge
elastic.bc.constant.type.yhizlo 3D Edge
elastic.bc.constant.type.yhizhi 3D Edge
elastic.bc.constant.type.zloxlo 3D Edge
elastic.bc.constant.type.zloxhi 3D Edge
elastic.bc.constant.type.zhixlo 3D Edge
elastic.bc.constant.type.zhixhi 3D Edge
elastic.bc.constant.type.xloylo 3D Edge / 2D Corner
elastic.bc.constant.type.xloyhi 3D Edge / 2D Corner
elastic.bc.constant.type.xhiylo 3D Edge / 2D Corner
elastic.bc.constant.type.xhiyhi 3D Edge / 2D Corner
elastic.bc.constant.type.xlo 3D Face / 2D Edge
elastic.bc.constant.type.xhi 3D Face / 2D Edge
elastic.bc.constant.type.ylo 3D Face / 2D Edge
elastic.bc.constant.type.yhi 3D Face / 2D Edge
elastic.bc.constant.type.zlo 3D Face
elastic.bc.constant.type.zhi 3D Face
elastic.bc.constant.val.xloylozlo 3D Corner
elastic.bc.constant.val.xloylozhi 3D Corner
elastic.bc.constant.val.xloyhizlo 3D Corner
elastic.bc.constant.val.xloyhizhi 3D Corner
elastic.bc.constant.val.xhiylozlo 3D Corner
elastic.bc.constant.val.xhiylozhi 3D Corner
elastic.bc.constant.val.xhiyhizlo 3D Corner
elastic.bc.constant.val.xhiyhizhi 3D Corner
elastic.bc.constant.val.ylozlo 3D Edge
elastic.bc.constant.val.ylozhi 3D Edge
elastic.bc.constant.val.yhizlo 3D Edge
elastic.bc.constant.val.yhizhi 3D Edge
elastic.bc.constant.val.zloxlo 3D Edge
elastic.bc.constant.val.zloxhi 3D Edge
elastic.bc.constant.val.zhixlo 3D Edge
elastic.bc.constant.val.zhixhi 3D Edge
elastic.bc.constant.val.xloylo 3D Edge / 2D Corner
elastic.bc.constant.val.xloyhi 3D Edge / 2D Corner
elastic.bc.constant.val.xhiylo 3D Edge / 2D Corner
elastic.bc.constant.val.xhiyhi 3D Edge / 2D Corner
elastic.bc.constant.val.xlo 3D Face / 2D Edge
elastic.bc.constant.val.xhi 3D Face / 2D Edge
elastic.bc.constant.val.ylo 3D Face / 2D Edge
elastic.bc.constant.val.yhi 3D Face / 2D Edge
elastic.bc.constant.val.zlo 3D Face
elastic.bc.constant.val.zhi 3D Face
elastic.bc.tensiontest.type Tension test type. uniaxial_stress_clamp uniaxial_kolsky uniaxial_stress uniaxial_strain
elastic.bc.tensiontest.disp Applied displacement (can be interpolator)
elastic.bc.tensiontest.trac Applied traction (can be interpolator)
elastic.print_model Print out model variables (if enabled by model) false
elastic.rhs.type initial condition for right hand side (body force)

elastic.rhs.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
elastic.rhs.expression.coord coordinate system to use cartesian polar
elastic.rhs.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
elastic.rhs.trig.nr Number of real (cosin) waves
elastic.rhs.trig.ni Number of imaginary (sin) waves
elastic.rhs.trig.dim Spatial dimension
elastic.rhs.trig.alpha Multiplier
elastic.interval Timestep interval for elastic solves (default - solve every time) 0
elastic.max_coarsening_level Maximum multigrid coarsening level (default - none, maximum coarsening) -1
elastic.print_residual Whether to include residual output field false
elastic.elastic_ref_threshold Whether to refine based on elastic solution 0.01
elastic.zero_out_displacement Set this to true to zero out the displacement before each solve. (This is a temporary fix - we need to figure out why this is needed.) false
elastic.tstart Time to start doing the elastic solve (by default, start immediately) -1.0
Tref Initial temperature for thermal expansion computation 300.0
model_ap.lambda model_ap.mu model_ap.E model_ap.nu model_ap.kappa Specify exactly 2: required
Lame constant \(\lambda\), shear modulus \(\mu\), Young's modulus \(E\), Poisson's ratio \(\nu\), bulk modulus \(K\). You can currently specify (mu and kappa), (lambda and mu), or (E and nu).
model_ap.F0 Large-deformation eigendeformation (Identity = no deformation)
model_ap.eps0 Small-deformation eigendeformation (Zero = no deformation)
model_htpb.lambda model_htpb.mu model_htpb.E model_htpb.nu model_htpb.kappa Specify exactly 2: required
Lame constant \(\lambda\), shear modulus \(\mu\), Young's modulus \(E\), Poisson's ratio \(\nu\), bulk modulus \(K\). You can currently specify (mu and kappa), (lambda and mu), or (E and nu).
model_htpb.F0 Large-deformation eigendeformation (Identity = no deformation)
model_htpb.eps0 Small-deformation eigendeformation (Zero = no deformation)
allow_unused Set this to true to allow unused inputs without error. (Not recommended.) false


Integrator::HeatConduction

Input name Description Value
heat.alpha Diffusion coefficient \(\alpha\). *This is an example of a required input variable - - program will terminate unless it is provided.* required
heat.refinement_threshold Criterion for mesh refinement. *This is an example of a default input variable. The default value is provided here, not in the definition of the variable.* 0.01
ic.type Initial condition type.

ic.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
ic.sphere.radius Radius of the sphere 1.0
ic.sphere.center Vector location of the sphere center
ic.sphere.inside Value of the field inside the sphere 1.0
ic.sphere.outside Value of the field outside teh sphere 0.0
ic.sphere.type Type - can be cylinder oriented along the x, y, z directions or full sphere. xyz yz zx xy
ic.expression.coord coordinate system to use cartesian polar
ic.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
bc.temp.type Select BC object for temperature

bc.temp.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
bc.temp.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
bc.temp.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
bc.temp.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
bc.temp.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.temp.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.temp.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
bc.temp.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
bc.temp.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
bc.temp.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
bc.temp.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
bc.temp.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0
bc.temp.expression.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
bc.temp.expression.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
bc.temp.expression.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
bc.temp.expression.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
bc.temp.expression.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.temp.expression.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
method Select between using a realspace solve or the spectral method realspace spectral


Integrator::Dendrite

Input name Description Value
alpha Pre-multiplier of "m" barrier height required
delta Anisotropy factor required
gamma Anisotropic temperature coupling factor required
diffusion Thermal constant 1.0
eps Diffuse boundary width required
tau Diffusive timescale required
theta Orientation about z axis (Deg) 0.0
heat.refinement_threshold Refinement criteria for temperature 0.01
phi.refinement_threshold Refinement criteria for phi 0.01
bc.temp.type boundary conditions for temperature field

bc.temp.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
bc.temp.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
bc.temp.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
bc.temp.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
bc.temp.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.temp.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.temp.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
bc.temp.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
bc.temp.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
bc.temp.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
bc.temp.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
bc.temp.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0
bc.phi.type boundary conditions for \(\phi\) field

bc.phi.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
bc.phi.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
bc.phi.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
bc.phi.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
bc.phi.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.phi.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
bc.phi.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
bc.phi.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
bc.phi.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
bc.phi.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
bc.phi.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
bc.phi.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0


Integrator::AllenCahn

Input name Description Value
refinement_threshold Criterion for mesh refinement [0.01] 0.01
ch.L Value for \(L\) (mobility) 1.0
ch.eps Value for \(\epsilon\) (diffuse boundary width) 0.1
ch.grad Value for \(\kappa\) (Interface energy parameter) 1.0
ch.chempot Value for \(\lambda\) (Chemical potential coefficient) 1.0
ch.direction Force directional growth: 0=no growth, 1=only positive, -1=only negative 0 1 -1
ch.direction_tstart Time to start forcing directional growth 0.0
alpha.ic.type Set the initial condition for the alpha field

alpha.ic.sphere.radius Radius of the sphere 1.0
alpha.ic.sphere.center Vector location of the sphere center
alpha.ic.sphere.inside Value of the field inside the sphere 1.0
alpha.ic.sphere.outside Value of the field outside teh sphere 0.0
alpha.ic.sphere.type Type - can be cylinder oriented along the x, y, z directions or full sphere. xyz yz zx xy
alpha.ic.constant.value Array of constant values. The number of values should equal either 1 or N where N is the number of fab components required
alpha.ic.expression.coord coordinate system to use cartesian polar
alpha.ic.expression.region# Mathematical expression in terms of x,y,z,t (if coord=cartesian) or r,theta,z,t (if coord=polar) and any defined constants. # = 0,1,2,...
alpha.ic.bmp.filename BMP filename. file path
alpha.ic.bmp.fit How to position image in space stretch fitheight fitwidth coord
alpha.ic.bmp.coord.lo Location of lower-left corner in the domain
alpha.ic.bmp.coord.hi Location of upper-right corner in the domain
alpha.ic.bmp.channel Color channel to use r g b R G B
alpha.ic.bmp.min Scaling value - minimum 0.0
alpha.ic.bmp.max Scaling value - maximum 255.0
alpha.ic.png.channel Color channel to use (options: r, R, g, G, b, B, a, A) r g b a R G B A
alpha.ic.png.filename BMP filename. file path
alpha.ic.png.fit how to position the image stretch fitheight fitwidth coord
alpha.ic.png.coord.lo Lower-left coordinates of image in domain
alpha.ic.png.coord.hi Upper-right coordinates of image in domain
alpha.ic.png.min Desired minimum value to scale pixels by 0.0
alpha.ic.png.max Desired maximum value to scale pixels by 255.0
alpha.ic.random.offset offset from the [0,1] random number range 0.0
alpha.ic.random.mult multiplier for the [0,1] random number range 1.0
alpha.ic.psread.eps Diffuseness of the sphere boundary
alpha.ic.psread.filename Location of .xyzr file file path
alpha.ic.psread.verbose Verbosity (used in parser only)
alpha.ic.psread.mult Coordinate multiplier
alpha.ic.psread.invert Coordinate multiplier
alpha.ic.psread.x0 Coordinate offset
alpha.bc.type Use a constant BC object for temperature value.bc = new BC::Constant(1); :ref:`BC::Constant` parameters

alpha.bc.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
alpha.bc.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
alpha.bc.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
alpha.bc.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
alpha.bc.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
alpha.bc.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
alpha.bc.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
alpha.bc.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
alpha.bc.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
alpha.bc.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
alpha.bc.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
alpha.bc.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0


Integrator::CahnHilliard

Input name Description Value
gamma Interface energy 0.0005
L Mobility 1.0
refinement_threshold Regridding criterion 1E100
eta.ic.type initial condition for \(\eta\)

eta.ic.random.offset offset from the [0,1] random number range 0.0
eta.ic.random.mult multiplier for the [0,1] random number range 1.0
eta.bc.type boundary condition for \(\eta\)

eta.bc.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
eta.bc.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
eta.bc.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
eta.bc.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
eta.bc.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
eta.bc.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
eta.bc.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
eta.bc.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
eta.bc.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
eta.bc.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
eta.bc.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
eta.bc.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0
method Which method to use - realspace or spectral method. realspace spectral


Integrator::PFC

Input name Description Value
q0 frequency term required
eps chemical potential width required
eta.ic.type initial condition for \(\eta\)

eta.ic.random.offset offset from the [0,1] random number range 0.0
eta.ic.random.mult multiplier for the [0,1] random number range 1.0
eta.bc.type boundary condition for \(\eta\)

eta.bc.constant.type.xlo BC type on the lower x edge (2d) face (3d) dirichlet
eta.bc.constant.type.xhi BC type on the upper x edge (2d) face (3d) dirichlet
eta.bc.constant.type.ylo BC type on the lower y edge (2d) face (3d) dirichlet
eta.bc.constant.type.yhi BC type on the upper y edge (2d) face (3d) dirichlet
eta.bc.constant.type.zlo BC type on the lower z face (processed but ignored in 2d to prevent unused input errors) dirichlet
eta.bc.constant.type.zhi BC type on the upper z face (processed but ignored in 2d to prevent unused input errors) dirichlet
eta.bc.constant.val.xlo BC value on the lower x edge (2d) face (3d) 0.0
eta.bc.constant.val.xhi BC value on the upper x edge (2d) face (3d) 0.0
eta.bc.constant.val.ylo BC value on the lower y edge (2d) face (3d) 0.0
eta.bc.constant.val.yhi BC value on the upper y edge (2d) face (3d) 0.0
eta.bc.constant.val.zlo BC value on the lower z face (processed but ignored in 2d to prevent unused input errors) 0.0
eta.bc.constant.val.zhi BC value on the upper z face (processed but ignored in 2d to prevent unused input errors) 0.0


:math:`\quad`