pyvale 2025.4.0__py3-none-any.whl → 2025.5.1__py3-none-any.whl

pyvale/simcases/case00_HEX8.i

@@ -0,0 +1,242 @@
+#-------------------------------------------------------------------------
+# pyvale: single element test 3D
+#-------------------------------------------------------------------------
+
+#-------------------------------------------------------------------------
+#_* MOOSEHERDER VARIABLES - START
+
+endTime = 20
+timeStep = 1
+
+# Geometric Properties
+lengX = 10e-3   # m
+lengY = 10e-3   # m
+lengZ = 10e-3   # m
+
+# Mesh Properties
+nElemX = 2
+nElemY = 2
+nElemZ = 2
+eType = HEX8 # TET4, TET10, TET11, HEX8, HEX20, HEX27
+
+# Thermal BCs
+coolantTemp=100.0      # degC
+heatTransCoeff=125.0e3 # W.m^-2.K^-1
+surfHeatFlux=4.67e6    # W.m^-2, taken from Adel's first paper
+timeConst = 1   # s
+
+# Mechanical Loads/BCs
+topDispRate = ${fparse 1e-3 / endTime}  # m/s
+
+# Thermal Props:
+Density = 8829.0  # kg.m^-3
+ThermCond = 384.0 # W.m^-1.K^-1
+SpecHeat = 406.0  # J.kg^-1.K^-1
+
+# Material Properties:
+EMod= 100e9     # Pa
+PRatio = 0.33    # -
+
+# Thermo-mechanical coupling
+stressFreeTemp = 20 # degC
+ThermExp = 17.8e-6 # 1/degC
+
+#** MOOSEHERDER VARIABLES - END
+#-------------------------------------------------------------------------
+
+[GlobalParams]
+    displacements = 'disp_x disp_y disp_z'
+[]
+
+[Mesh]
+    [generated]
+        type = GeneratedMeshGenerator
+        dim = 3
+        nx = ${nElemX}
+        ny = ${nElemY}
+        nz = ${nElemZ}
+        xmax = ${lengX}
+        ymax = ${lengY}
+        zmax = ${lengZ}
+        elem_type = ${eType}
+    []
+[]
+
+[Variables]
+    [temperature]
+      family = LAGRANGE
+      order = FIRST
+      initial_condition = ${coolantTemp}
+    []
+[]
+
+[Kernels]
+    [heat_conduction]
+      type = HeatConduction
+      variable = temperature
+    []
+    [time_derivative]
+      type = HeatConductionTimeDerivative
+      variable = temperature
+    []
+[]
+
+
+[Physics/SolidMechanics/QuasiStatic]
+    [all]
+        strain = SMALL
+        incremental = true
+        add_variables = true
+        material_output_family = MONOMIAL   # MONOMIAL, LAGRANGE
+        material_output_order = FIRST       # CONSTANT, FIRST, SECOND,
+        generate_output = 'strain_xx strain_yy strain_zz strain_xy strain_yz strain_xz'
+    []
+[]
+
+[BCs]
+    [heat_flux_in]
+        type = FunctionNeumannBC
+        variable = temperature
+        boundary = 'top'
+        function = '${fparse surfHeatFlux}*(1-exp(-(1/${timeConst})*t))'
+    []
+    [heat_flux_out]
+        type = ConvectiveHeatFluxBC
+        variable = temperature
+        boundary = 'bottom'
+        T_infinity = ${coolantTemp}
+        heat_transfer_coefficient = ${heatTransCoeff}
+    []
+
+    [bottom_x]
+        type = DirichletBC
+        variable = disp_x
+        boundary = 'bottom'
+        value = 0.0
+    []
+    [bottom_y]
+        type = DirichletBC
+        variable = disp_y
+        boundary = 'bottom'
+        value = 0.0
+    []
+    [bottom_z]
+        type = DirichletBC
+        variable = disp_z
+        boundary = 'bottom'
+        value = 0.0
+    []
+    [top_x]
+        type = DirichletBC
+        variable = disp_x
+        boundary = 'top'
+        value = 0.0
+    []
+    [top_y]
+        type = FunctionDirichletBC
+        variable = disp_y
+        boundary = 'top'
+        function = '${topDispRate}*t'
+    []
+    [top_z]
+        type = DirichletBC
+        variable = disp_z
+        boundary = 'top'
+        value = 0.0
+    []
+[]
+
+[Materials]
+    [mat_thermal]
+        type = HeatConductionMaterial
+        thermal_conductivity = ${ThermCond}
+        specific_heat = ${SpecHeat}
+    []
+    [mat_density]
+        type = GenericConstantMaterial
+        prop_names = 'density'
+        prop_values = ${Density}
+    []
+    [mat_expansion]
+        type = ComputeThermalExpansionEigenstrain
+        temperature = temperature
+        stress_free_temperature = ${stressFreeTemp}
+        thermal_expansion_coeff = ${ThermExp}
+        eigenstrain_name = thermal_expansion_eigenstrain
+    []
+
+    [mat_elasticity]
+        type = ComputeIsotropicElasticityTensor
+        youngs_modulus = ${EMod}
+        poissons_ratio = ${PRatio}
+    []
+    [stress]
+        type =  ComputeFiniteStrainElasticStress
+    []
+[]
+
+[Preconditioning]
+    [SMP]
+        type = SMP
+        full = true
+    []
+[]
+
+[Executioner]
+    type = Transient
+
+    solve_type = 'NEWTON'
+    petsc_options = '-snes_converged_reason'
+    petsc_options_iname = '-pc_type -pc_hypre_type'
+    petsc_options_value = 'hypre boomeramg'
+
+    l_max_its = 1000
+    l_tol = 1e-6
+
+    nl_max_its = 50
+    nl_rel_tol = 1e-6
+    nl_abs_tol = 1e-6
+
+    start_time=0.0
+    end_time = ${endTime}
+    dt = ${timeStep}
+
+    [Predictor]
+      type = SimplePredictor
+      scale = 1
+    []
+[]
+
+
+[Postprocessors]
+    [react_y_bot]
+        type = SidesetReaction
+        direction = '0 1 0'
+        stress_tensor = stress
+        boundary = 'bottom'
+    []
+    [react_y_top]
+        type = SidesetReaction
+        direction = '0 1 0'
+        stress_tensor = stress
+        boundary = 'top'
+    []
+
+    [disp_y_max]
+        type = NodalExtremeValue
+        variable = disp_y
+    []
+    [disp_x_max]
+        type = NodalExtremeValue
+        variable = disp_x
+    []
+    [disp_z_max]
+        type = NodalExtremeValue
+        variable = disp_z
+    []
+
+[]
+
+[Outputs]
+    exodus = true
+[]

pyvale/simcases/case00_TET10.i

@@ -5,7 +5,7 @@
 #-------------------------------------------------------------------------
 #_* MOOSEHERDER VARIABLES - START
 
-endTime = 50
+endTime = 20
 timeStep = 1
 
 # Geometric Properties
@@ -89,7 +89,7 @@ ThermExp = 17.8e-6 # 1/degC
         add_variables = true
         material_output_family = MONOMIAL   # MONOMIAL, LAGRANGE
         material_output_order = FIRST       # CONSTANT, FIRST, SECOND,
-        generate_output = 'stress_xx stress_yy stress_zz stress_xy stress_yz stress_xz strain_xx strain_yy strain_zz strain_xy strain_yz strain_xz'
+        generate_output = 'strain_xx strain_yy strain_zz strain_xy strain_yz strain_xz'
     []
 []
 

pyvale/simcases/case00_TET14.i

@@ -5,7 +5,7 @@
 #-------------------------------------------------------------------------
 #_* MOOSEHERDER VARIABLES - START
 
-endTime = 50
+endTime = 20
 timeStep = 1
 
 # Geometric Properties
@@ -89,7 +89,7 @@ ThermExp = 17.8e-6 # 1/degC
         add_variables = true
         material_output_family = MONOMIAL   # MONOMIAL, LAGRANGE
         material_output_order = FIRST       # CONSTANT, FIRST, SECOND,
-        generate_output = 'stress_xx stress_yy stress_zz stress_xy stress_yz stress_xz strain_xx strain_yy strain_zz strain_xy strain_yz strain_xz'
+        generate_output = 'strain_xx strain_yy strain_zz strain_xy strain_yz strain_xz'
     []
 []
 

pyvale/simcases/case00_TET4.i

@@ -0,0 +1,242 @@
+#-------------------------------------------------------------------------
+# pyvale: single element test 3D
+#-------------------------------------------------------------------------
+
+#-------------------------------------------------------------------------
+#_* MOOSEHERDER VARIABLES - START
+
+endTime = 20
+timeStep = 1
+
+# Geometric Properties
+lengX = 10e-3   # m
+lengY = 10e-3   # m
+lengZ = 10e-3   # m
+
+# Mesh Properties
+nElemX = 1
+nElemY = 1
+nElemZ = 1
+eType = TET4 # TET4, TET10, TET11, HEX8, HEX20, HEX27
+
+# Thermal BCs
+coolantTemp=100.0      # degC
+heatTransCoeff=125.0e3 # W.m^-2.K^-1
+surfHeatFlux=4.67e6    # W.m^-2, taken from Adel's first paper
+timeConst = 1   # s
+
+# Mechanical Loads/BCs
+topDispRate = ${fparse 1e-3 / endTime}  # m/s
+
+# Thermal Props:
+Density = 8829.0  # kg.m^-3
+ThermCond = 384.0 # W.m^-1.K^-1
+SpecHeat = 406.0  # J.kg^-1.K^-1
+
+# Material Properties:
+EMod= 100e9     # Pa
+PRatio = 0.33    # -
+
+# Thermo-mechanical coupling
+stressFreeTemp = 20 # degC
+ThermExp = 17.8e-6 # 1/degC
+
+#** MOOSEHERDER VARIABLES - END
+#-------------------------------------------------------------------------
+
+[GlobalParams]
+    displacements = 'disp_x disp_y disp_z'
+[]
+
+[Mesh]
+    [generated]
+        type = GeneratedMeshGenerator
+        dim = 3
+        nx = ${nElemX}
+        ny = ${nElemY}
+        nz = ${nElemZ}
+        xmax = ${lengX}
+        ymax = ${lengY}
+        zmax = ${lengZ}
+        elem_type = ${eType}
+    []
+[]
+
+[Variables]
+    [temperature]
+      family = LAGRANGE
+      order = FIRST
+      initial_condition = ${coolantTemp}
+    []
+[]
+
+[Kernels]
+    [heat_conduction]
+      type = HeatConduction
+      variable = temperature
+    []
+    [time_derivative]
+      type = HeatConductionTimeDerivative
+      variable = temperature
+    []
+[]
+
+
+[Physics/SolidMechanics/QuasiStatic]
+    [all]
+        strain = SMALL
+        incremental = true
+        add_variables = true
+        material_output_family = MONOMIAL   # MONOMIAL, LAGRANGE
+        material_output_order = FIRST       # CONSTANT, FIRST, SECOND,
+        generate_output = 'strain_xx strain_yy strain_zz strain_xy strain_yz strain_xz'
+    []
+[]
+
+[BCs]
+    [heat_flux_in]
+        type = FunctionNeumannBC
+        variable = temperature
+        boundary = 'top'
+        function = '${fparse surfHeatFlux}*(1-exp(-(1/${timeConst})*t))'
+    []
+    [heat_flux_out]
+        type = ConvectiveHeatFluxBC
+        variable = temperature
+        boundary = 'bottom'
+        T_infinity = ${coolantTemp}
+        heat_transfer_coefficient = ${heatTransCoeff}
+    []
+
+    [bottom_x]
+        type = DirichletBC
+        variable = disp_x
+        boundary = 'bottom'
+        value = 0.0
+    []
+    [bottom_y]
+        type = DirichletBC
+        variable = disp_y
+        boundary = 'bottom'
+        value = 0.0
+    []
+    [bottom_z]
+        type = DirichletBC
+        variable = disp_z
+        boundary = 'bottom'
+        value = 0.0
+    []
+    [top_x]
+        type = DirichletBC
+        variable = disp_x
+        boundary = 'top'
+        value = 0.0
+    []
+    [top_y]
+        type = FunctionDirichletBC
+        variable = disp_y
+        boundary = 'top'
+        function = '${topDispRate}*t'
+    []
+    [top_z]
+        type = DirichletBC
+        variable = disp_z
+        boundary = 'top'
+        value = 0.0
+    []
+[]
+
+[Materials]
+    [mat_thermal]
+        type = HeatConductionMaterial
+        thermal_conductivity = ${ThermCond}
+        specific_heat = ${SpecHeat}
+    []
+    [mat_density]
+        type = GenericConstantMaterial
+        prop_names = 'density'
+        prop_values = ${Density}
+    []
+    [mat_expansion]
+        type = ComputeThermalExpansionEigenstrain
+        temperature = temperature
+        stress_free_temperature = ${stressFreeTemp}
+        thermal_expansion_coeff = ${ThermExp}
+        eigenstrain_name = thermal_expansion_eigenstrain
+    []
+
+    [mat_elasticity]
+        type = ComputeIsotropicElasticityTensor
+        youngs_modulus = ${EMod}
+        poissons_ratio = ${PRatio}
+    []
+    [stress]
+        type =  ComputeFiniteStrainElasticStress
+    []
+[]
+
+[Preconditioning]
+    [SMP]
+        type = SMP
+        full = true
+    []
+[]
+
+[Executioner]
+    type = Transient
+
+    solve_type = 'NEWTON'
+    petsc_options = '-snes_converged_reason'
+    petsc_options_iname = '-pc_type -pc_hypre_type'
+    petsc_options_value = 'hypre boomeramg'
+
+    l_max_its = 1000
+    l_tol = 1e-6
+
+    nl_max_its = 50
+    nl_rel_tol = 1e-6
+    nl_abs_tol = 1e-6
+
+    start_time=0.0
+    end_time = ${endTime}
+    dt = ${timeStep}
+
+    [Predictor]
+      type = SimplePredictor
+      scale = 1
+    []
+[]
+
+
+[Postprocessors]
+    [react_y_bot]
+        type = SidesetReaction
+        direction = '0 1 0'
+        stress_tensor = stress
+        boundary = 'bottom'
+    []
+    [react_y_top]
+        type = SidesetReaction
+        direction = '0 1 0'
+        stress_tensor = stress
+        boundary = 'top'
+    []
+
+    [disp_y_max]
+        type = NodalExtremeValue
+        variable = disp_y
+    []
+    [disp_x_max]
+        type = NodalExtremeValue
+        variable = disp_x
+    []
+    [disp_z_max]
+        type = NodalExtremeValue
+        variable = disp_z
+    []
+
+[]
+
+[Outputs]
+    exodus = true
+[]

pyvale/simcases/run_1case.py

@@ -15,7 +15,7 @@ from mooseherder import (MooseConfig,
 
 #===============================================================================
 # Change this to run a different case
-CASE_STR = 'case16'
+CASE_STR = 'case00_HEX27'
 #===============================================================================
 
 CASE_FILES = (CASE_STR+'.geo',CASE_STR+'.i')

pyvale/simtools.py

@@ -0,0 +1,67 @@
+# ==============================================================================
+# pyvale: the python validation engine
+# License: MIT
+# Copyright (C) 2025 The Computer Aided Validation Team
+# ==============================================================================
+import numpy as np
+from pyvale.rendermesh import RenderMeshData
+
+class SimTools:
+    """Namespace for tools required for analysing simulation results.
+    """
+
+    @staticmethod
+    def centre_mesh_nodes(nodes: np.ndarray, spat_dim: int) -> np.ndarray:
+        """A method to centre the nodes of a mesh around the origin.
+
+        Parameters
+        ----------
+        nodes : np.ndarray
+            An array containing the node locations of the mesh.
+        spat_dim : int
+            The spatial dimension of the mesh.
+
+        Returns
+        -------
+        np.ndarray
+            An array containing the mesh node locations, but centred around
+            the origin.
+        """
+        max = np.max(nodes, axis=0)
+        min = np.min(nodes, axis=0)
+        middle = max - ((max - min) / 2)
+        if spat_dim == 3:
+            middle[2] = 0
+        centred = np.subtract(nodes, middle)
+        return centred
+
+    @staticmethod
+    def get_deformed_nodes(timestep: int,
+                           render_mesh: RenderMeshData) -> np.ndarray | None:
+        """A method to obtain the deformed locations of all the nodes at a given
+            timestep.
+
+        Parameters
+        ----------
+        timestep : int
+            The timestep at which to find the deformed nodes.
+        render_mesh: RenderMeshData
+            A dataclass containing the skinned mesh and simulation results.
+
+        Returns
+        -------
+        np.ndarray | None
+            An array containing the deformed values of all the components at
+            each node location. Returns None if there are no deformation values.
+        """
+        if render_mesh.fields_disp is None:
+            return None
+
+        added_disp = render_mesh.fields_disp[:, timestep]
+        if added_disp.shape[1] == 2:
+            added_disp = np.hstack((added_disp,np.zeros([added_disp.shape[0],1])))
+        coords = np.delete(render_mesh.coords, 3, axis=1)
+        deformed_nodes = coords + added_disp
+        return deformed_nodes
+
+