Merge branch 'misc-improvements' into less-shell-scripts

python/damask/_result.py

@@ -568,9 +568,8 @@ class Result:
                 'label': 'sigma',
                 'meta':  {
                           'Unit':        P['meta']['Unit'],
-                          'Description': 'Cauchy stress calculated from {} ({}) '.format(P['label'],
+                          'Description': 'Cauchy stress calculated from {} ({}) and {} ({})'\
-                                                                                         P['meta']['Description'])+\
+                                         .format(P['label'],P['meta']['Description'],F['label'],F['meta']['Description']),
-                                         'and {} ({})'.format(F['label'],F['meta']['Description']),
                           'Creator':     inspect.stack()[0][3][1:]
                           }
                 }
@@ -638,17 +637,24 @@ class Result:
 
 
     @staticmethod
-    def _add_eigenvalue(T_sym):
+    def _add_eigenvalue(T_sym,eigenvalue):
+        if   eigenvalue == 'max':
+            label,p = 'Maximum',2
+        elif eigenvalue == 'mid':
+            label,p = 'Intermediate',1
+        elif eigenvalue == 'min':
+            label,p = 'Minimum',0
+
         return {
-                'data': mechanics.eigenvalues(T_sym['data']),
+                'data': mechanics.eigenvalues(T_sym['data'])[:,p],
-                'label': 'lambda({})'.format(T_sym['label']),
+                'label': 'lambda_{}({})'.format(eigenvalue,T_sym['label']),
                 'meta' : {
                           'Unit':         T_sym['meta']['Unit'],
-                          'Description': 'Eigenvalues of {} ({})'.format(T_sym['label'],T_sym['meta']['Description']),
+                          'Description': '{} eigenvalue of {} ({})'.format(label,T_sym['label'],T_sym['meta']['Description']),
                           'Creator':     inspect.stack()[0][3][1:]
                          }
                 }
-    def add_eigenvalues(self,T_sym):
+    def add_eigenvalue(self,T_sym,eigenvalue='max'):
         """
         Add eigenvalues of symmetric tensor.
 
@@ -656,33 +662,46 @@ class Result:
         ----------
         T_sym : str
             Label of symmetric tensor dataset.
+        eigenvalue : str, optional
+            Eigenvalue. Select from ‘max’, ‘mid’, ‘min’. Defaults to ‘max’.
 
         """
-        self._add_generic_pointwise(self._add_eigenvalue,{'T_sym':T_sym})
+        self._add_generic_pointwise(self._add_eigenvalue,{'T_sym':T_sym},{'eigenvalue':eigenvalue})
 
 
     @staticmethod
-    def _add_eigenvector(T_sym):
+    def _add_eigenvector(T_sym,eigenvalue):
+        if   eigenvalue == 'max':
+            label,p = 'maximum',2
+        elif eigenvalue == 'mid':
+            label,p = 'intermediate',1
+        elif eigenvalue == 'min':
+            label,p = 'minimum',0
+        print('p',eigenvalue)
         return {
-                'data': mechanics.eigenvectors(T_sym['data']),
+                'data': mechanics.eigenvectors(T_sym['data'])[:,p],
-                'label': 'v({})'.format(T_sym['label']),
+                'label': 'v_{}({})'.format(eigenvalue,T_sym['label']),
                 'meta' : {
                           'Unit':        '1',
-                          'Description': 'Eigenvectors of {} ({})'.format(T_sym['label'],T_sym['meta']['Description']),
+                          'Description': 'Eigenvector corresponding to {} eigenvalue of {} ({})'\
+                                         .format(label,T_sym['label'],T_sym['meta']['Description']),
                           'Creator':     inspect.stack()[0][3][1:]
                          }
                 }
-    def add_eigenvectors(self,T_sym):
+    def add_eigenvector(self,T_sym,eigenvalue='max'):
         """
-        Add eigenvectors of symmetric tensor.
+        Add eigenvector of symmetric tensor.
 
         Parameters
         ----------
         T_sym : str
             Label of symmetric tensor dataset.
+        eigenvalue : str, optional
+            Eigenvalue to which the eigenvector corresponds. Select from
+            ‘max’, ‘mid’, ‘min’. Defaults to ‘max’.
 
         """
-        self._add_generic_pointwise(self._add_eigenvector,{'T_sym':T_sym})
+        self._add_generic_pointwise(self._add_eigenvector,{'T_sym':T_sym},{'eigenvalue':eigenvalue})
 
 
     @staticmethod
@@ -819,9 +838,8 @@ class Result:
                 'label': 'S',
                 'meta':  {
                           'Unit':        P['meta']['Unit'],
-                          'Description': '2. Kirchhoff stress calculated from {} ({}) '.format(P['label'],
+                          'Description': '2. Piola-Kirchhoff stress calculated from {} ({}) and {} ({})'\
-                                                                                               P['meta']['Description'])+\
+                                         .format(P['label'],P['meta']['Description'],F['label'],F['meta']['Description']),
-                                         'and {} ({})'.format(F['label'],F['meta']['Description']),
                           'Creator':     inspect.stack()[0][3][1:]
                           }
                 }

python/tests/reference/Result/12grains6x7x8.geom

@@ -1,68 +1,4 @@
-68 header
+4 header
-geom_fromVoronoiTessellation 2.0.3-1073-g6f3cb071 
-<texture>
-[Grain1]
-(gauss)	phi1 358.98	Phi 65.62	phi2 24.48
-[Grain2]
-(gauss)	phi1 121.05	Phi 176.11	phi2 295.73
-[Grain3]
-(gauss)	phi1 43.79	Phi 113.76	phi2 345.90
-[Grain4]
-(gauss)	phi1 265.15	Phi 62.52	phi2 299.71
-[Grain5]
-(gauss)	phi1 221.23	Phi 26.54	phi2 207.05
-[Grain6]
-(gauss)	phi1 249.81	Phi 61.47	phi2 152.14
-[Grain7]
-(gauss)	phi1 332.45	Phi 99.16	phi2 345.34
-[Grain8]
-(gauss)	phi1 312.27	Phi 118.27	phi2 181.59
-[Grain9]
-(gauss)	phi1 303.10	Phi 48.21	phi2 358.03
-[Grain10]
-(gauss)	phi1 338.26	Phi 48.11	phi2 176.78
-[Grain11]
-(gauss)	phi1 115.17	Phi 56.54	phi2 223.84
-[Grain12]
-(gauss)	phi1 281.04	Phi 97.48	phi2 27.94
-<microstructure>
-[Grain1]
-crystallite 1
-(constituent)	phase 1	texture 1	fraction 1.0
-[Grain2]
-crystallite 1
-(constituent)	phase 1	texture 2	fraction 1.0
-[Grain3]
-crystallite 1
-(constituent)	phase 1	texture 3	fraction 1.0
-[Grain4]
-crystallite 1
-(constituent)	phase 1	texture 4	fraction 1.0
-[Grain5]
-crystallite 1
-(constituent)	phase 1	texture 5	fraction 1.0
-[Grain6]
-crystallite 1
-(constituent)	phase 1	texture 6	fraction 1.0
-[Grain7]
-crystallite 1
-(constituent)	phase 1	texture 7	fraction 1.0
-[Grain8]
-crystallite 1
-(constituent)	phase 1	texture 8	fraction 1.0
-[Grain9]
-crystallite 1
-(constituent)	phase 1	texture 9	fraction 1.0
-[Grain10]
-crystallite 1
-(constituent)	phase 1	texture 10	fraction 1.0
-[Grain11]
-crystallite 1
-(constituent)	phase 1	texture 11	fraction 1.0
-[Grain12]
-crystallite 1
-(constituent)	phase 1	texture 12	fraction 1.0
-<!skip>
 grid   a 6 b 7 c 8
 size   x 0.75 y 0.875 z 1.0
 origin x 0.0 y 0.0 z 0.0

python/tests/reference/Result/6grains6x7x8_single_phase.geom

@@ -0,0 +1,61 @@
+4 header
+grid   a 6 b 7 c 8
+size   x 0.75 y 0.875 z 1.0
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
+3 3 3 4 3 3
+3 1 1 1 3 3
+3 5 1 1 1 3
+1 5 5 1 1 1
+1 5 5 1 1 1
+6 3 3 4 1 6
+6 3 3 4 4 6
+6 3 3 1 3 3
+3 1 1 1 3 3
+3 1 1 1 1 1
+1 1 1 1 1 1
+6 6 3 1 1 1
+6 3 3 3 6 6
+6 3 3 3 6 6
+6 3 3 1 1 6
+3 1 1 1 1 3
+6 1 1 1 2 2
+1 6 2 2 2 2
+6 6 2 2 2 6
+6 3 3 3 6 6
+6 3 3 3 6 6
+5 6 6 6 1 6
+6 6 6 6 2 2
+6 6 6 2 2 2
+2 6 2 2 2 2
+6 5 2 2 2 2
+6 5 5 2 2 6
+5 5 5 3 6 6
+5 5 6 6 6 5
+6 6 6 6 6 6
+6 6 6 6 2 2
+4 4 6 2 2 2
+4 4 2 2 2 2
+5 5 5 2 2 2
+5 5 5 5 2 5
+5 5 5 4 4 5
+6 6 6 6 4 4
+4 4 5 5 2 4
+4 4 5 2 2 4
+4 4 2 2 2 2
+5 5 5 2 2 2
+5 5 5 4 4 5
+5 5 4 4 4 3
+4 5 5 5 4 3
+4 4 5 5 5 4
+4 4 5 5 2 4
+4 4 2 2 2 2
+5 5 2 2 2 2
+5 5 4 4 4 4
+3 4 4 4 4 3
+3 5 5 4 3 3
+4 5 5 5 3 3
+4 5 5 5 1 1
+4 4 5 2 1 1
+6 4 4 4 4 1
+3 4 4 4 4 3

python/tests/reference/Result/material.config

@@ -124,6 +124,3 @@ a_slip                  2.25
 h0_slipslip             75e6
 interaction_slipslip    1 1 1.4 1.4 1.4 1.4
 atol_resistance         1
-
-<crystallite>
-[dummy]

python/tests/test_Result.py

@@ -20,6 +20,13 @@ def default(tmp_path,reference_dir):
     f.pick('times',20.0)
     return f
 
+@pytest.fixture
+def single_phase(tmp_path,reference_dir):
+    """Single phase Result file in temp location for modification."""
+    fname = '6grains6x7x8_single_phase_tensionY.hdf5'
+    shutil.copy(os.path.join(reference_dir,fname),tmp_path)
+    return Result(os.path.join(tmp_path,fname))
+
 @pytest.fixture
 def reference_dir(reference_dir_base):
     """Directory containing reference results."""
@@ -125,21 +132,23 @@ class TestResult:
         in_file   = default.read_dataset(loc['s_P'],0)
         assert np.allclose(in_memory,in_file)
 
-    def test_add_eigenvalues(self,default):
+    @pytest.mark.parametrize('eigenvalue,function',[('max',np.amax),('min',np.amin)])
+    def test_add_eigenvalue(self,default,eigenvalue,function):
         default.add_Cauchy('P','F')
-        default.add_eigenvalues('sigma')
+        default.add_eigenvalue('sigma',eigenvalue)
-        loc = {'sigma'        :default.get_dataset_location('sigma'),
+        loc = {'sigma' :default.get_dataset_location('sigma'),
-               'lambda(sigma)':default.get_dataset_location('lambda(sigma)')}
+               'lambda':default.get_dataset_location('lambda_{}(sigma)'.format(eigenvalue))}
-        in_memory = mechanics.eigenvalues(default.read_dataset(loc['sigma'],0))
+        in_memory = function(mechanics.eigenvalues(default.read_dataset(loc['sigma'],0)),axis=1,keepdims=True)
-        in_file   = default.read_dataset(loc['lambda(sigma)'],0)
+        in_file   = default.read_dataset(loc['lambda'],0)
         assert np.allclose(in_memory,in_file)
 
-    def test_add_eigenvectors(self,default):
+    @pytest.mark.parametrize('eigenvalue,idx',[('max',2),('mid',1),('min',0)])
+    def test_add_eigenvector(self,default,eigenvalue,idx):
         default.add_Cauchy('P','F')
-        default.add_eigenvectors('sigma')
+        default.add_eigenvector('sigma',eigenvalue)
         loc = {'sigma'   :default.get_dataset_location('sigma'),
-               'v(sigma)':default.get_dataset_location('v(sigma)')}
+               'v(sigma)':default.get_dataset_location('v_{}(sigma)'.format(eigenvalue))}
-        in_memory = mechanics.eigenvectors(default.read_dataset(loc['sigma'],0))
+        in_memory = mechanics.eigenvectors(default.read_dataset(loc['sigma'],0))[:,idx]
         in_file   = default.read_dataset(loc['v(sigma)'],0)
         assert np.allclose(in_memory,in_file)
 
@@ -296,3 +305,7 @@ class TestResult:
     def test_vtk(self,tmp_path,default,output):
         os.chdir(tmp_path)
         default.to_vtk(output)
+
+    def test_XDMF(self,tmp_path,single_phase):
+        os.chdir(tmp_path)
+        single_phase.write_XDMF