Test outstanding generate phase field input methods for CIPHER

matflow/data/scripts/cipher/generate_phase_field_input_from_random_voronoi_orientations.py

@@ -1,3 +1,6 @@
+from matflow.param_classes.orientations import Orientations
+import numpy as np
+
 from cipher_parse import (
     CIPHERInput,
     MaterialDefinition,
@@ -21,7 +24,12 @@ def generate_phase_field_input_from_random_voronoi_orientations(
     interface_binning,
     combine_phases,
 ):
-    quats = orientations["quaternions"]
+    try:
+        quats = orientations["quaternions"]
+    except TypeError:
+        # Convert to old matflow format
+        orientations = _convert_orientations_to_old_matflow_format(orientations)
+        quats = orientations["quaternions"]
 
     # initialise `MaterialDefinition`, `InterfaceDefinition` and
     # `PhaseTypeDefinition` objects:
@@ -63,3 +71,40 @@ def generate_phase_field_input_from_random_voronoi_orientations(
     phase_field_input = inp.to_JSON(keep_arrays=True)
 
     return {"phase_field_input": phase_field_input}
+
+
+# This code is copied from dream3D/generate_volume_element_statistics.py
+def _convert_orientations_to_old_matflow_format(orientations: Orientations):
+    # see `LatticeDirection` enum:
+    align_lookup = {
+        "A": "a",
+        "B": "b",
+        "C": "c",
+        "A_STAR": "a*",
+        "B_STAR": "b*",
+        "C_STAR": "c*",
+    }
+    unit_cell_alignment = {
+        "x": align_lookup[orientations.unit_cell_alignment.x.name],
+        "y": align_lookup[orientations.unit_cell_alignment.y.name],
+        "z": align_lookup[orientations.unit_cell_alignment.z.name],
+    }
+    type_lookup = {
+        "QUATERNION": "quat",
+        "EULER": "euler",
+    }
+    type_ = type_lookup[orientations.representation.type.name]
+    oris = {
+        "type": type_,
+        "unit_cell_alignment": unit_cell_alignment,
+    }
+
+    if type_ == "quat":
+        quat_order = orientations.representation.quat_order.name.lower().replace("_", "-")
+        oris["quaternions"] = np.array(orientations.data)
+        oris["quat_component_ordering"] = quat_order
+    elif type_ == "euler":
+        oris["euler_angles"] = np.array(orientations.data)
+        oris["euler_degrees"] = orientations.representation.euler_is_degrees
+
+    return oris

matflow/data/template_components/task_schemas.yaml

@@ -2228,6 +2228,7 @@
   - parameter: solution_parameters
   - parameter: orientation_gradient
   - parameter: random_seed
+    default_value: null
   - parameter: is_periodic
   - parameter: interface_binning
     default_value: null

matflow/data/workflows/grain_growth_from_voronoi_with_texture_binned.yaml

@@ -0,0 +1,72 @@
+name: grain_growth_from_voronoi_with_texture_binned
+
+tasks:  
+- schema: sample_texture_random_mtex
+  inputs:
+      specimen_symmetry: cubic
+      num_orientations: 1000
+      crystal_symmetry: cubic
+      execution_mode: script
+- schema: generate_phase_field_input_from_random_voronoi_with_orientations
+  inputs:
+    is_periodic: false
+    num_phases: 200
+    grid_size: [256, 256]
+    size: [256, 256]
+    materials:
+      - name: sub-grain-matrix
+        properties:
+          chemicalenergy: none
+          molarvolume: 1e-5
+          temperature0: 500.0
+    interfaces:
+      - materials: [sub-grain-matrix, sub-grain-matrix] 
+        properties:
+          width: 4.0
+          energy:
+            e0: 1.0e+8
+          mobility:
+            m0: 10.0e-11
+    components: [ti]
+    outputs: [phaseid, matid, interfaceid, 0_phi]
+    solution_parameters:
+      abstol: 0.0001
+      amrinterval: 25
+      initblocksize: [1, 1]
+      initcoarsen: 8
+      initrefine: 8
+      interpolation: cubic
+      maxnrefine: 8
+      minnrefine: 0
+      outfile: out
+      outputfreq: 100
+      petscoptions: -ts_adapt_monitor -ts_rk_type 2a
+      random_seed: 1579993586
+      reltol: 0.0001
+      time: 10_000
+    interface_binning: # specify one or both of energy_range/mobility_range:
+      base_interface_name: sub-grain-matrix-sub-grain-matrix
+      theta_max: 35
+      bin_width: 1
+      energy_range: [0.1e+8, 1.0e+8]
+      # mobility_range: [1.0e-11, 10.0e-11]
+      # n: 1 # mobility parameter
+      # B: 5 # mobility parameter
+
+- schema: simulate_grain_growth
+  inputs:
+    VTU_files_time_interval: 1_000
+    derive_outputs:
+      - name: num_voxels_per_phase 
+    save_outputs:
+      - name: phaseid 
+        time_interval: 1_000
+      - name: matid
+        number: 4
+      - name: interfaceid
+        number: 4
+      - name: 0_phi
+        number: 4
+      - name: num_voxels_per_phase
+        time_interval: 1_000
+    delete_VTUs: true

matflow/data/workflows/grain_growth_from_voronoi_with_texture_gradient.yaml

@@ -0,0 +1,69 @@
+name: grain_growth_from_voronoi_with_texture_gradient
+
+tasks:  
+- schema: generate_phase_field_input_from_random_voronoi_with_orientations_gradient
+  inputs:
+    is_periodic: false
+    num_phases: 200
+    grid_size: [256, 256]
+    size: [256, 256]
+    materials:
+      - name: sub-grain-matrix
+        properties:
+          chemicalenergy: none
+          molarvolume: 1e-5
+          temperature0: 500.0
+    interfaces:
+      - materials: [sub-grain-matrix, sub-grain-matrix] 
+        properties:
+          width: 4.0
+          energy:
+            e0: 1.0e+8
+          mobility:
+            m0: 10.0e-11
+    components: [ti]
+    outputs: [phaseid, matid, interfaceid, 0_phi]
+    solution_parameters:
+      abstol: 0.0001
+      amrinterval: 25
+      initblocksize: [1, 1]
+      initcoarsen: 8
+      initrefine: 8
+      interpolation: cubic
+      maxnrefine: 8
+      minnrefine: 0
+      outfile: out
+      outputfreq: 100
+      petscoptions: -ts_adapt_monitor -ts_rk_type 2a
+      random_seed: 1579993586
+      reltol: 0.0001
+      time: 10_000
+    orientation_gradient:
+      max_misorientation_deg: 20
+      add_highly_misoriented_grain: true
+    interface_binning: # specify one or both of energy_range/mobility_range:
+      base_interface_name: sub-grain-matrix-sub-grain-matrix
+      theta_max: 35
+      bin_width: 1
+      energy_range: [0.1e+8, 1.0e+8]
+      # mobility_range: [1.0e-11, 10.0e-11]
+      # n: 1 # mobility parameter
+      # B: 5 # mobility parameter
+
+- schema: simulate_grain_growth
+  inputs:
+    VTU_files_time_interval: 1_000
+    derive_outputs:
+      - name: num_voxels_per_phase 
+    save_outputs:
+      - name: phaseid 
+        time_interval: 1_000
+      - name: matid
+        number: 4
+      - name: interfaceid
+        number: 4
+      - name: 0_phi
+        number: 4
+      - name: num_voxels_per_phase
+        time_interval: 1_000
+    delete_VTUs: true