feat/material tracking

pyproject.toml

@@ -27,6 +27,8 @@ dependencies = [
 "fans" = "aiida_fans.calculations:FansCalculation"
 [project.entry-points."aiida.parsers"]
 "fans" = "aiida_fans.parsers:FansParser"
+[project.entry-points."aiida.data"]
+"fans" = "aiida_fans.data:MaterialData"
 
 # Build System
 [build-system]

src/aiida_fans/calculations.py

@@ -1,4 +1,4 @@
-"""CalcJob subclasses for aiida-fans calculations."""
+"""Subclasses of CalcJob for aiida-fans calculations."""
 
 from json import dump
 from pathlib import Path
@@ -11,6 +11,7 @@
 from aiida.orm import Dict, Float, Int, List, SinglefileData, Str
 from h5py import File as h5File
 
+from aiida_fans.data import MaterialData
 from aiida_fans.helpers import make_input_dict
 
 
@@ -47,7 +48,8 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
         ## Problem Type and Material Model
         spec.input("problem_type", valid_type=Str)
         spec.input("matmodel", valid_type=Str)
-        spec.input("material_properties", valid_type=Dict)
+        spec.input("material_phases", valid_type=Dict)
+        spec.input_namespace("material_properties", valid_type=MaterialData, dynamic=True)
         ## Solver Settings
         spec.input("method", valid_type=Str)
         spec.input("n_it", valid_type=Int)

src/aiida_fans/data.py

@@ -0,0 +1,17 @@
+"""Subclasses of Data for aiida-fans."""
+
+from aiida.orm import Data
+
+
+class MaterialData(Data):
+    """Data class to represent material properties."""
+
+    def __init__(self, **kwargs):
+        """Initialize the MaterialData instance."""
+        bulk = kwargs.pop("bulk_modulus", None)
+        shear = kwargs.pop("shear_modulus", None)
+        super().__init__(**kwargs)
+        if bulk is not None:
+            self.base.attributes.set("bulk_modulus", bulk)
+        if shear is not None:
+            self.base.attributes.set("shear_modulus", shear)

src/aiida_fans/helpers.py

@@ -19,7 +19,10 @@ def make_input_dict(job: CalcJob) -> dict[str, Any]:
         ## Problem Type and Material Model
         "problem_type": job.inputs.problem_type.value,
         "matmodel": job.inputs.matmodel.value,
-        "material_properties": job.inputs.material_properties.get_dict(),
+        "material_properties": {
+            "bulk_modulus": [mat.base.attributes.get("bulk_modulus") for mat in job.inputs.material_properties],
+            "shear_modulus": [mat.base.attributes.get("shear_modulus") for mat in job.inputs.material_properties],
+        },
         ## Solver Settings
         "method": job.inputs.method.value,
         "n_it": job.inputs.n_it.value,

src/aiida_fans/parsers.py

@@ -1,4 +1,4 @@
-"""Parser subclass for aiida-fans calculations."""
+"""Subclass of Parser for aiida-fans calculations."""
 
 from pathlib import Path
 

src/aiida_fans/readme_submit.py

@@ -0,0 +1,83 @@
+"""This is an example submit script. It should **not** be committed to dev."""
+
+from aiida import load_profile  # type: ignore
+from aiida.orm import load_code, load_node
+from aiida.tools import delete_nodes
+
+from aiida_fans.utils import run_fans
+
+load_profile()
+
+
+################################################################################
+
+inputs = {
+    "code": load_code("FANS"),  #! Code node goes here.
+    "microstructure": {
+        "file": load_node(label="microstructure.file"),  #! Microstructure node goes here.
+        "datasetname": "/dset_0/image",
+        "L": [1.0, 1.0, 1.0]
+    },
+    "results_prefix": "my_results",  #? Optional
+    "problem_type": "mechanical",
+    "matmodel": "LinearElasticIsotropic",
+
+    ######################################
+    # Proposed material properties format:
+    "material_phases": {
+        "copper": [0, 2],
+        "aluminium": [1]
+    },
+    # translates to: phase 0 = copper, phase 1 = aluminium, phase 2 = copper
+    #
+    # Under this format, each material would be its own node labelled "copper",
+    # "aluminium", etc., and they would be of various MaterialData types that
+    # the plugin defines for each supported matmodel.
+    #
+    # Additionally, each job would have a material_phases input which defines
+    # what materials occupy which phases of the microstructure. If the user were
+    # to provide materials inconsistent with the provided "matmodel", utils
+    # could reject the input without ever calling AiiDA or FANS.
+    #
+    # If an advanced user wishes to use a custom material, they must create the
+    # node themselves and provide it a unique label. That label can then simply
+    # be used in place of "copper" or "alumininum" above.
+    ######################################
+
+    "method": "cg",
+    "error_parameters": {
+        "measure": "Linfinity",
+        "type": "absolute",
+        "tolerance": 1e-10
+    },
+    "n_it": 100,
+    "macroscale_loading": [
+        {
+            "strain_indices": [      2, 3, 4, 5],
+            "stress_indices": [0, 1            ],
+            "strain": [[0.005, 0.0, 0.0, 0.0],[0.010, 0.0, 0.0, 0.0]],
+            "stress": [[0.0, 0.0],[0.0, 0.0]]
+        },
+        {
+            "strain_indices": [            4, 5],
+            "stress_indices": [0, 1, 2, 3      ],
+            "strain": [[0.001, 0.005],[0.005, 0.001]],
+            "stress": [[0.01, 0.0, 0.0, 0.0],[0.0, 0.01, 0.0, 0.0]]
+        }
+    ],
+    "results": [  # Optional
+        "stress", "strain",
+        "stress_average", "strain_average",
+        "phase_stress_average", "phase_strain_average",
+        "microstructure", "displacement", "absolute_error",
+    ],
+
+    "metadata": {  # Optional
+        # "label": "test calculation 1",
+        # "dry_run": True
+    }
+}
+
+################################################################################
+
+run_fans(inputs)