Merge branch 'development' into vector-mechanics

VERSION

@@ -1 +1 @@
-v3.0.0-alpha-777-g523a0979e
+v3.0.0-alpha-791-g662a033d9

processing/pre/geom_grainGrowth.py

@@ -15,8 +15,8 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 
-getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0)                               # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
+getInterfaceEnergy = lambda A,B: np.float32((A != B)*1.0)                                           # 1.0 if A & B are distinct, 0.0 otherwise
-struc = ndimage.generate_binary_structure(3,1)                                                     # 3D von Neumann neighborhood
+struc = ndimage.generate_binary_structure(3,1)                                                      # 3D von Neumann neighborhood
 
 
 #--------------------------------------------------------------------------------------------------
@@ -62,7 +62,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
   damask.util.report(scriptName,name)
 
-  geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+  geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
   grid_original = geom.grid
   damask.util.croak(geom)
@@ -174,4 +174,4 @@ for name in filenames:
               origin    = geom.origin,
               comments  = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
              )\
-        .save_ASCII(sys.stdout if name is None else name)
+        .save(sys.stdout if name is None else name)

processing/pre/mentat_pbcOnBoxMesh.py

@@ -11,8 +11,6 @@ import numpy as np
 
 import damask
 
-sys.path.append(str(damask.solver.Marc().library_path))
-
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
@@ -235,6 +233,7 @@ if remote and filenames != []:
 if filenames == []: filenames = [None]
 
 if remote:
+  sys.path.append(str(damask.solver.Marc().library_path))
   import py_mentat
 
   damask.util.report(scriptName, 'waiting to connect...')

processing/pre/mentat_spectralBox.py

@@ -9,7 +9,6 @@ import damask
 
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
-sys.path.append(str(damask.solver.Marc().library_path))
 
 #-------------------------------------------------------------------------------------------------
 def outMentat(cmd,locals):
@@ -185,9 +184,10 @@ parser.set_defaults(port = None,
 
 if options.port is not None:
     try:
+        sys.path.append(str(damask.solver.Marc().library_path))
         import py_mentat
     except ImportError:
-        parser.error('no valid Mentat release found.')
+        parser.error('no valid Mentat release found')
 
 # --- loop over input files ------------------------------------------------------------------------
 
@@ -196,7 +196,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     material = geom.material.flatten(order='F')
 
     cmds = [\

python/damask/_geom.py

@@ -213,9 +213,8 @@ class Geom:
         if not keyword.startswith('head') or header_length < 3:
             raise TypeError('Header length information missing or invalid')
 
-        content = f.readlines()
-
         comments = []
+        content = f.readlines()
         for i,line in enumerate(content[:header_length]):
             items = line.split('#')[0].lower().strip().split()
             key = items[0] if items else ''
@@ -228,7 +227,7 @@ class Geom:
             else:
                 comments.append(line.strip())
 
-        material = np.empty(grid.prod())                                                      # initialize as flat array
+        material = np.empty(grid.prod())                                                            # initialize as flat array
         i = 0
         for line in content[header_length:]:
             items = line.split('#')[0].split()
@@ -246,8 +245,8 @@ class Geom:
         if i != grid.prod():
             raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
 
-        if not np.any(np.mod(material,1) != 0.0):                                             # no float present
+        if not np.any(np.mod(material,1) != 0.0):                                                   # no float present
-            material = material.astype('int')
+            material = material.astype('int') - (1 if material.min() > 0 else 0)
 
         return Geom(material.reshape(grid,order='F'),size,origin,comments)
 
@@ -510,7 +509,7 @@ class Geom:
 
         Parameters
         ----------
-        fname : str or or pathlib.Path
+        fname : str or pathlib.Path
             Filename to write. Valid extension is .vtr, it will be appended if not given.
         compress : bool, optional
             Compress with zlib algorithm. Defaults to True.

python/damask/_orientation.py

@@ -803,7 +803,7 @@ class Orientation(Rotation):
             return np.all(components >= 0.0,axis=-1)
 
 
-    def IPF_color(self,vector,proper=False):
+    def IPF_color(self,vector,in_SST=True,proper=False):
         """
         Map vector to RGB color within standard stereographic triangle of own symmetry.
 
@@ -811,6 +811,9 @@ class Orientation(Rotation):
         ----------
         vector : numpy.ndarray of shape (...,3)
             Vector to colorize.
+        in_SST : bool, optional
+            Consider symmetrically equivalent orientations such that poles are located in SST.
+            Defaults to True.
         proper : bool, optional
             Consider only vectors with z >= 0, hence combine two neighboring SSTs (with mirrored colors).
             Defaults to False.
@@ -825,7 +828,7 @@ class Orientation(Rotation):
         Inverse pole figure color of the e_3 direction for a crystal in "Cube" orientation with cubic symmetry:
 
         >>> o = damask.Orientation(lattice='cubic')
-        >>> o.IPF_color(o.to_SST([0,0,1]))
+        >>> o.IPF_color([0,0,1])
         array([1., 0., 0.])
 
         References
@@ -1076,7 +1079,7 @@ class Orientation(Rotation):
 
 
     @classmethod
-    def Bravais_to_Miller(cls,uvtw=None,hkil=None):
+    def Bravais_to_Miller(cls,*,uvtw=None,hkil=None):
         """
         Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
 
@@ -1104,7 +1107,7 @@ class Orientation(Rotation):
 
 
     @classmethod
-    def Miller_to_Bravais(cls,uvw=None,hkl=None):
+    def Miller_to_Bravais(cls,*,uvw=None,hkl=None):
         """
         Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).
 
@@ -1133,7 +1136,7 @@ class Orientation(Rotation):
         return np.einsum('il,...l',basis,axis)
 
 
-    def to_lattice(self,direction=None,plane=None):
+    def to_lattice(self,*,direction=None,plane=None):
         """
         Calculate lattice vector corresponding to crystal frame direction or plane normal.
 
@@ -1157,7 +1160,7 @@ class Orientation(Rotation):
         return np.einsum('il,...l',basis,axis)
 
 
-    def to_frame(self,uvw=None,hkl=None,with_symmetry=False):
+    def to_frame(self,*,uvw=None,hkl=None,with_symmetry=False):
         """
         Calculate crystal frame vector along lattice direction [uvw] or plane normal (hkl).
 
@@ -1185,7 +1188,7 @@ class Orientation(Rotation):
                 np.einsum('il,...l',basis,axis))
 
 
-    def to_pole(self,uvw=None,hkl=None,with_symmetry=False):
+    def to_pole(self,*,uvw=None,hkl=None,with_symmetry=False):
         """
         Calculate lab frame vector along lattice direction [uvw] or plane normal (hkl).
 

python/damask/_result.py

@@ -747,7 +747,7 @@ class Result:
                                     'hex':'hP'}[q['meta']['Lattice']])
 
         return {
-                'data': np.uint8(o.IPF_color(o.to_SST(l))*255),
+                'data': np.uint8(o.IPF_color(l)*255),
                 'label': 'IPFcolor_[{} {} {}]'.format(*m),
                 'meta' : {
                           'Unit':        '8-bit RGB',

python/tests/test_Geom.py

@@ -74,6 +74,7 @@ class TestGeom:
 
     def test_save_load_ASCII(self,default,tmp_path):
         default.save_ASCII(tmp_path/'ASCII')
+        default.material -= 1
         assert geom_equal(Geom.load_ASCII(tmp_path/'ASCII'),default)
 
     def test_invalid_origin(self,default):

python/tests/test_Orientation.py

@@ -231,11 +231,11 @@ class TestOrientation:
     @pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
     @pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
     @pytest.mark.parametrize('proper',[True,False])
-    def test_IPF_color_vectorization(self,lattice,shape,vector,proper):
+    @pytest.mark.parametrize('in_SST',[True,False])
+    def test_IPF_color_vectorization(self,lattice,shape,vector,proper,in_SST):
         o = Orientation.from_random(lattice=lattice,shape=shape)
-        poles = o.to_SST(vector=vector,proper=proper)
+        for r, theO in zip(o.IPF_color(vector,in_SST=in_SST,proper=proper).reshape((-1,3)),o.flatten()):
-        for r, theO in zip(o.IPF_color(poles,proper=proper).reshape((-1,3)),o.flatten()):
+            assert np.allclose(r,theO.IPF_color(vector,in_SST=in_SST,proper=proper))
-            assert np.allclose(r,theO.IPF_color(theO.to_SST(vector=vector,proper=proper),proper=proper))
 
     @pytest.mark.parametrize('lattice',Orientation.crystal_families)
     @pytest.mark.parametrize('a,b',[
@@ -263,14 +263,14 @@ class TestOrientation:
         cube = Orientation(lattice='cubic')
         for direction in set(permutations(np.array(color['direction']))):
             assert np.allclose(np.array(color['RGB']),
-                               cube.IPF_color(cube.to_SST(vector=np.array(direction),proper=proper),proper=proper))
+                               cube.IPF_color(vector=np.array(direction),proper=proper))
 
     @pytest.mark.parametrize('lattice',Orientation.crystal_families)
     @pytest.mark.parametrize('proper',[True,False])
     def test_IPF_equivalent(self,set_of_quaternions,lattice,proper):
         direction = np.random.random(3)*2.0-1.0
         o = Orientation(rotation=set_of_quaternions,lattice=lattice).equivalent
-        color = o.IPF_color(o.to_SST(vector=direction,proper=proper),proper=proper)
+        color = o.IPF_color(vector=direction,proper=proper)
         assert np.allclose(np.broadcast_to(color[0,...],color.shape),color)
 
     @pytest.mark.parametrize('lattice',Orientation.crystal_families)

python/tests/test_Result.py

@@ -178,7 +178,7 @@ class TestResult:
                         lattice={'fcc':'cF',
                                  'bcc':'cI',
                                  'hex':'hP'}[crystal_structure])
-        in_memory = np.uint8(c.IPF_color(c.to_SST(np.array(d)))*255)
+        in_memory = np.uint8(c.IPF_color(np.array(d))*255)
         in_file = default.read_dataset(loc['color'])
         assert np.allclose(in_memory,in_file)