Merge branch 'main' into dependabot/pip/matplotlib-3.9.1

.ci_support/environment-notebooks-integration.yml

@@ -10,8 +10,8 @@ dependencies:
 - k3d
 - matplotlib =3.8.4
 - numpy =1.26.4
-- pyiron_base =0.9.5
-- pyiron_snippets =0.1.2
+- pyiron_base =0.9.10
+- pyiron_snippets =0.1.3
 - pyiron-data =0.0.30
 - python-damask =3.0.0b
 - scipy =1.14.0
@@ -28,3 +28,4 @@ dependencies:
 - trame-vuetify =2.5.0
 - sympy =1.12.1
 - python-blosc2
+- mendeleev =0.17.0

.ci_support/environment-pypi-unit.yml

@@ -6,9 +6,10 @@ dependencies:
 - codacy-coverage
 - matplotlib =3.8.4
 - numpy =1.26.4
-- pyiron_base =0.9.5
-- pyiron_snippets =0.1.2
+- pyiron_base =0.9.10
+- pyiron_snippets =0.1.3
 - scipy =1.14.0
 - sympy =1.12.1
 - python-blosc2
 - python-damask =3.0.0b
+- mendeleev =0.17.0

pyiron_continuum/damask/damaskjob.py

@@ -111,7 +111,7 @@ def set_homogenization(self, **kwargs):
         """
         self.input.homogenization = DAMASKCreator.homogenization(**kwargs)
 
-    def set_phase(self, composition, lattice, output_list):
+    def set_phase(self, composition, lattice, output_list=None):
         """
 
         Args:

pyiron_continuum/damask/factory.py

@@ -10,6 +10,7 @@
 ) as damask_alarm:
     from damask import GeomGrid, YAML, ConfigMaterial, seeds, Rotation
 import numpy as np
+import mendeleev
 
 __author__ = "Muhammad Hassani"
 __copyright__ = (
@@ -191,27 +192,33 @@ def homogenization(method, parameters):
         """
         return {method: parameters}
 
+
     @staticmethod
-    def phase(composition, lattice, output_list, elasticity, plasticity=None):
+    def phase(composition, elasticity, plasticity=None, lattice=None, output_list=None):
         """
         Returns a dictionary describing the phases for damask.
         Args:
             composition(str)
-            lattice(dict)
+            lattice(str)
             output_list(str)
             elasticity(dict)
             plasticity(dict)
         Examples:
             phase = phase(
                 composition='Aluminum',
                 lattice='cF',
-                output_list='[F, P, F_e, F_p, L_p, O]',
                 elasticity=elasticity,
                 plasticity=plasticity
             )
 
         For the details of isotropic model, one can refer to https://doi.org/10.1016/j.scriptamat.2017.09.047
         """
+        if lattice is None:
+            lattice = {"BCC": "cI", "HEX": "hP", "FCC": "cF"}[
+                composition_to_spacegroup(composition)
+            ]
+        if output_list is None:
+            output_list = ["F", "P", "F_e", "F_p", "L_p", "O"]
         d = {
             composition: {
                 "lattice": lattice,
@@ -310,3 +317,19 @@ def rotation(method="from_random", *args, **kwargs):
         if isinstance(method, str):
             method = getattr(Rotation, method)
         return method(*args, **kwargs)
+
+
+def get_element_abbreviation(name):
+    if len(name) <= 2:
+        return name
+    from mendeleev.fetch import fetch_table
+    el_table = fetch_table('elements')
+    cond = el_table['name'] == name
+    if not any(cond):
+        raise NameError(name, "does not exist")
+    return el_table[cond].iloc[0]['symbol']
+
+
+def composition_to_spacegroup(composition):
+    abbreviation = get_element_abbreviation(composition)
+    return mendeleev.element(abbreviation).lattice_structure

pyiron_continuum/damask/regrid.py

@@ -35,7 +35,7 @@ def grid_coords_point_initial(self):
     @cached_property
     def d5Out(self):
         d5Out = damask.Result(self.load_name)
-        increments = int(d5Out.increments[-1].split("_")[-1])
+        increments = int(str(d5Out.increments[-1]).split("_")[-1])
         d5Out = d5Out.view(increments=increments)
         return d5Out
 

pyiron_continuum/project.py

@@ -56,12 +56,16 @@ def material(rotation, elements, phase, homogenization):
         return DAMASKCreator.material(rotation, elements, phase, homogenization)
 
     @staticmethod
-    def phase(composition, lattice, output_list, elasticity, plasticity):
+    def phase(composition, lattice, elasticity, plasticity, output_list=None):
         warnings.warn(
             "Setting phase via project creator is deprecated. Use job.set_phase instead"
         )
         return DAMASKCreator.phase(
-            composition, lattice, output_list, elasticity, plasticity
+            composition=composition,
+            lattice=lattice,
+            output_list=output_list,
+            elasticity=elasticity,
+            plasticity=plasticity
         )
 
     @staticmethod

pyiron_continuum/toolkit.py

@@ -8,7 +8,7 @@
 from pyiron_base import Toolkit, Project, JobFactoryCore
 from pyiron_continuum.fenics.job.generic import Fenics
 from pyiron_continuum.fenics.job.elastic import FenicsLinearElastic
-from pyiron_continuum.project import DAMASKCreator
+from pyiron_continuum.damask.factory import Create as DAMASKCreator
 from pyiron_continuum.schroedinger.schroedinger import TISE
 from pyiron_continuum.mesh import RectMesh
 from pyiron_continuum.schroedinger.potentials import Sinusoidal, SquareWell
@@ -99,7 +99,7 @@ def Homogenization(method, parameters):
         return DAMASKCreator.homogenization(method, parameters)
 
     @staticmethod
-    def Phase(composition, lattice, output_list, elasticity, plasticity):
+    def Phase(composition, lattice, elasticity, plasticity, output_list=None):
         """
         returns a dictionary describing the phases for damask
         Args:
@@ -123,8 +123,12 @@ def Phase(composition, lattice, output_list, elasticity, plasticity):
                                     xi_inf_sl=[63e6])
         """
         return DAMASKCreator.phase(
-            composition, lattice, output_list, elasticity, plasticity
-        )
+            composition=composition,
+            lattice=lattice,
+            output_list=output_list,
+            elasticity=elasticity,
+            plasticity=plasticity,
+    )
 
     @staticmethod
     def Elasticity(**kwargs):

setup.py

@@ -34,8 +34,8 @@
     install_requires=[
         'matplotlib==3.9.1',
         'numpy==1.26.4',
-        'pyiron_base==0.9.5',
-        'pyiron_snippets==0.1.2',
+        'pyiron_base==0.9.10',
+        'pyiron_snippets==0.1.3',
         'scipy==1.14.0',
         'sympy==1.12.1'
     ],

tests/integration/damask/test_backward_compatibility.py

@@ -197,7 +197,7 @@ def get_load_step(reduction_speed, reduction_height, reduction_outputs):
             }
 
         job_name = "multiple_rolling"
-        job = self.project.create.job.Damask(job_name + "_0")
+        job = self.project.create.job.DAMASK(job_name + "_0")
         plasticity = self.get_plasticity_phenopowerlaw()
         grains = 4
         phase = self.get_phase_aluminum(self._get_elasticity(), plasticity)

tests/unit/damask/test_damaskjob.py

@@ -5,6 +5,7 @@
 import unittest
 from pyiron_base._tests import PyironTestCase
 from pyiron_continuum import Project
+from pyiron_continuum.damask.factory import composition_to_spacegroup
 
 
 class TestDamask(PyironTestCase):
@@ -60,6 +61,12 @@ def test_set_phase(self):
         )
         self.assertIsInstance(job.input.phase, dict)
 
+    def test_composition_to_spacegroup(self):
+        self.assertEqual(composition_to_spacegroup("Aluminum"), "FCC")
+        self.assertEqual(composition_to_spacegroup("Iron"), "BCC")
+        self.assertEqual(composition_to_spacegroup("Magnesium"), "HEX")
+        self.assertRaises(NameError, composition_to_spacegroup, "Frodo")
+
     @classmethod
     def tearDownClass(cls):
         cls.project.remove(enable=True)