Merge pull request #362 from pyiron/code_abstraction_damask

Code abstraction damask

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=None):
+    def set_phase(self, composition, lattice=None, output_list=None):
         """
 
         Args:

pyiron_continuum/damask/factory.py

@@ -10,7 +10,7 @@
 ) as damask_alarm:
     from damask import GeomGrid, YAML, ConfigMaterial, seeds, Rotation
 import numpy as np
-import mendeleev
+from pyiron_continuum.reference.mendeleev import get_atom_info
 
 __author__ = "Muhammad Hassani"
 __copyright__ = (
@@ -215,10 +215,13 @@ def phase(composition, elasticity, plasticity=None, lattice=None, output_list=No
         """
         if lattice is None:
             lattice = {"BCC": "cI", "HEX": "hP", "FCC": "cF"}[
-                composition_to_spacegroup(composition)
+                get_atom_info(name=composition)["lattice_structure"]
             ]
         if output_list is None:
-            output_list = ["F", "P", "F_e", "F_p", "L_p", "O"]
+            if plasticity is None:
+                output_list = ["F", "P", "F_e"]
+            else:
+                output_list = ["F", "P", "F_e", "F_p", "L_p", "O"]
         d = {
             composition: {
                 "lattice": lattice,
@@ -317,19 +320,3 @@ 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/project.py

@@ -56,7 +56,7 @@ def material(rotation, elements, phase, homogenization):
         return DAMASKCreator.material(rotation, elements, phase, homogenization)
 
     @staticmethod
-    def phase(composition, lattice, elasticity, plasticity, output_list=None):
+    def phase(composition, elasticity, plasticity=None, lattice=None, output_list=None):
         warnings.warn(
             "Setting phase via project creator is deprecated. Use job.set_phase instead"
         )

pyiron_continuum/toolkit.py

@@ -99,7 +99,7 @@ def Homogenization(method, parameters):
         return DAMASKCreator.homogenization(method, parameters)
 
     @staticmethod
-    def Phase(composition, lattice, elasticity, plasticity, output_list=None):
+    def Phase(composition, elasticity, plasticity=None, lattice=None, output_list=None):
         """
         returns a dictionary describing the phases for damask
         Args:

tests/unit/damask/test_damaskjob.py

@@ -5,7 +5,6 @@
 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):
@@ -61,12 +60,6 @@ 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)