Merge remote-tracking branch 'origin/development' into 2d-table-yaml

PRIVATE

@@ -1 +1 @@
-Subproject commit 13dfa0ee9d702782f0b7999f3f7fb2384f58d768
+Subproject commit 6abcd3dba91f37c747eae04c6695949e819ec54b

VERSION

@@ -1 +1 @@
-v3.0.0-alpha2-602-ge2d4ab427
+v3.0.0-alpha2-662-gb36ff26cb

examples/ConfigFiles/Phase_Dislotwin_TWIP-Steel-FeMnC.yaml

@@ -1,8 +1,8 @@
 TWIP_Steel_FeMnC:
   lattice: cF
-  mechanics:
+  mechanical:
-    elasticity: {type: hooke, C_11: 175.0e9, C_12: 115.0e9, C_44: 135.0e9}
+    elastic: {type: hooke, C_11: 175.0e9, C_12: 115.0e9, C_44: 135.0e9}
-    plasticity:
+    plastic:
       type: dislotwin
       output: [rho_mob, rho_dip, gamma_sl, Lambda_sl, tau_pass, f_tw, Lambda_tw, tau_hat_tw, f_tr]
       D: 2.0e-5

examples/ConfigFiles/Phase_Dislotwin_Tungsten.yaml

@@ -1,8 +1,8 @@
 Tungsten:
   lattice: cI
-  mechanics:
+  mechanical:
-    elasticity: {type: hooke, C_11: 523.0e9, C_12: 202.0e9, C_44: 161.0e9} # Marinica et al. Journal of Physics: Condensed Matter(2013)
+    elastic: {type: hooke, C_11: 523.0e9, C_12: 202.0e9, C_44: 161.0e9} # Marinica et al. Journal of Physics: Condensed Matter(2013)
-    plasticity:
+    plastic:
       type: dislotwin
       D: 2.0e-5              # Average grain size / m
       N_sl: [12]

examples/ConfigFiles/Phase_Isotropic_AluminumIsotropic.yaml

@@ -1,10 +1,10 @@
 # Kuo, J. C., Mikrostrukturmechanik von Bikristallen mit Kippkorngrenzen. Shaker-Verlag 2004. http://edoc.mpg.de/204079
 Aluminum:
   lattice: aP
-  mechanics:
+  mechanical:
     output: [F, P, F_e, F_p, L_p]
-    elasticity: {type: hooke, C_11: 110.9e9, C_12: 58.34e9}
+    elastic: {type: hooke, C_11: 110.9e9, C_12: 58.34e9}
-    plasticity:
+    plastic:
       type: isotropic
       output: [xi]
       xi_0: 31e6

examples/ConfigFiles/Phase_Isotropic_FreeSurface.yaml

@@ -1,9 +1,9 @@
-Air:
+FreeSurface:
   lattice: aP
-  mechanics:
+  mechanical:
     output: [F, P, F_e, F_p, L_p]
-    elasticity: {type: hooke, C_11: 1e8, C_12: 1e6}
+    elastic: {type: hooke, C_11: 1e8, C_12: 1e6}
-    plasticity:
+    plastic:
       type: isotropic
       output: [xi]
       xi_0: 0.3e6

examples/ConfigFiles/Phase_Phenopowerlaw_Aluminum.yaml

@@ -1,9 +1,9 @@
 Aluminum:
   lattice: cF
-  mechanics:
+  mechanical:
     output: [F, P, F_e, F_p, L_p, O]
-    elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
+    elastic: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
-    plasticity:
+    plastic:
       N_sl: [12]
       a_sl: 2.25
       dot_gamma_0_sl: 0.001

examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Ferrite.yaml

@@ -3,9 +3,9 @@
 # Diehl et.al. 2015 Meccanica
 Ferrite:
   lattice: cI
-  mechanics:
+  mechanical:
-    elasticity: {C_11: 233.3e9, C_12: 135.5e9, C_44: 118.0e9, type: hooke}
+    elastic: {C_11: 233.3e9, C_12: 135.5e9, C_44: 118.0e9, type: hooke}
-    plasticity:
+    plastic:
       N_sl: [12, 12]
       a_sl: 2.0
       dot_gamma_0_sl: 0.001

examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.yaml

@@ -3,9 +3,9 @@
 # Diehl et.al. 2015 Meccanica
 Martensite:
   lattice: cI
-  mechanics:
+  mechanical:
-    elasticity: {C_11: 417.4e9, C_12: 242.4e9, C_44: 211.1e9, type: hooke}
+    elastic: {C_11: 417.4e9, C_12: 242.4e9, C_44: 211.1e9, type: hooke}
-    plasticity:
+    plastic:
       N_sl: [12, 12]
       a_sl: 2.0
       dot_gamma_0_sl: 0.001

examples/ConfigFiles/Phase_Phenopowerlaw_Gold.yaml

@@ -5,10 +5,10 @@
 
 Gold:
   lattice: cF
-  mechanics:
+  mechanical:
     output: [F, P, F_e, F_p, L_p, O]
-    elasticity: {type: hooke, C_11: 191e9, C_12: 162e9, C_44: 42.2e9}
+    elastic: {type: hooke, C_11: 191e9, C_12: 162e9, C_44: 42.2e9}
-    plasticity:
+    plastic:
       type: phenopowerlaw
       output: [xi_sl]
       N_sl: [12]

examples/ConfigFiles/Phase_Phenopowerlaw_Magnesium.yaml

@@ -2,10 +2,10 @@
 Magnesium:
   lattice: hP
   c/a: 1.62350
-  mechanics:
+  mechanical:
     output: [F, P, F_e, F_p, L_p, O]
-    elasticity: {C_11: 59.3e9, C_12: 25.7e9, C_13: 21.4e9, C_33: 61.5e9, C_44: 16.4e9, type: hooke}
+    elastic: {C_11: 59.3e9, C_12: 25.7e9, C_13: 21.4e9, C_33: 61.5e9, C_44: 16.4e9, type: hooke}
-    plasticity:
+    plastic:
       N_sl: [3, 3, 0, 6, 0, 6]
       N_tw: [6, 0, 0, 6]
       h_0_tw_tw: 50.0e6
@@ -20,9 +20,6 @@ Magnesium:
       xi_0_sl: [10.0e6, 55.0e6, 0, 60.0e6, 0.0, 60.0e6]
       xi_inf_sl: [40.0e6, 135.0e6, 0, 150.0e6, 0.0, 150.0e6]
       xi_0_tw: [40e6, 0.0, 0.0, 60.0e6]
-####################################################
-# open for discussion
-####################################################
       a_sl: 2.25
       dot_gamma_0_sl: 0.001
       dot_gamma_0_tw: 0.001

examples/ConfigFiles/Phase_Phenopowerlaw_cpTi.yaml

@@ -4,10 +4,10 @@
 cpTi:
   lattice: hP
   c/a: 1.587
-  mechanics:
+  mechanical:
     output: [F, P, F_e, F_p, L_p, O]
-    elasticity: {C_11: 160.0e9, C_12: 90.0e9, C_13: 66.0e9, C_33: 181.7e9, C_44: 46.5e9, type: hooke}
+    elastic: {C_11: 160.0e9, C_12: 90.0e9, C_13: 66.0e9, C_33: 181.7e9, C_44: 46.5e9, type: hooke}
-    plasticity:
+    plastic:
       N_sl: [3, 3, 0, 6, 12]
       a_sl: 2.0
       dot_gamma_0_sl: 0.001

examples/grid/material.yaml

@@ -2,7 +2,7 @@
 homogenization:
   SX:
     N_constituents: 1
-    mechanics: {type: pass}
+    mechanical: {type: pass}
 
 material:
   - homogenization: SX
@@ -109,10 +109,10 @@ material:
 phase:
   Aluminum:
     lattice: cF
-    mechanics:
+    mechanical:
       output: [F, P, F_e, F_p, L_p, O]
-      elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
+      elastic: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
-      plasticity:
+      plastic:
         N_sl: [12]
         a_sl: 2.25
         atol_xi: 1.0

processing/post/DADF5_postResults.py

@@ -35,10 +35,10 @@ for filename in options.filenames:
     if not results.structured: continue
     coords = damask.grid_filters.coordinates0_point(results.cells,results.size,results.origin).reshape(-1,3,order='F')
 
-    N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
+    N_digits = int(np.floor(np.log10(int(results.increments[-1][10:]))))+1
     N_digits = 5 # hack to keep test intact
     for inc in damask.util.show_progress(results.iterate('increments'),len(results.increments)):
-        table = damask.Table(np.ones(np.product(results.cells),dtype=int)*int(inc[3:]),{'inc':(1,)})\
+        table = damask.Table(np.ones(np.product(results.cells),dtype=int)*int(inc[10:]),{'inc':(1,)})\
                       .add('pos',coords.reshape(-1,3))
 
         results.view('homogenizations',False)
@@ -59,5 +59,5 @@ for filename in options.filenames:
         if not os.path.isdir(dirname):
             os.mkdir(dirname,0o755)
         file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0],
-                                         inc[3:].zfill(N_digits))
+                                         inc[10:].zfill(N_digits))
         table.save(os.path.join(dirname,file_out),legacy=True)

processing/pre/geom_fromDREAM3D.py

@@ -65,7 +65,7 @@ if filenames == []: parser.error('no input file specified.')
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    geom = damask.Grid.load_DREAM3D(name,options.basegroup,options.pointwise)
+    geom = damask.Grid.load_DREAM3D(name,'FeatureIds')
     damask.util.croak(geom)
 
     geom.save_ASCII(os.path.splitext(name)[0]+'.geom')

python/damask/_colormap.py

@@ -27,11 +27,13 @@ class Colormap(mpl.colors.ListedColormap):
 
     References
     ----------
-    [1] DAMASK colormap theory
+    K. Moreland, Proceedings of the 5th International Symposium on Advances in Visual Computing, 2009
-      https://www.kennethmoreland.com/color-maps/ColorMapsExpanded.pdf
+    https://doi.org/10.1007/978-3-642-10520-3_9
-    [2] DAMASK colormaps first use
+
+    P. Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013
     https://doi.org/10.1016/j.ijplas.2012.09.012
-    [3] Matplotlib colormaps overview
+
+    Matplotlib colormaps overview
     https://matplotlib.org/tutorials/colors/colormaps.html
 
     """
@@ -524,7 +526,7 @@ class Colormap(mpl.colors.ListedColormap):
 
         References
         ----------
-        http://www.ryanjuckett.com/programming/rgb-color-space-conversion
+        https://www.easyrgb.com/en/math.php
 
         """
         rgb_lin = np.dot(np.array([
@@ -544,7 +546,7 @@ class Colormap(mpl.colors.ListedColormap):
 
         References
         ----------
-        http://www.ryanjuckett.com/programming/rgb-color-space-conversion
+        https://www.easyrgb.com/en/math.php
 
         """
         rgb_lin = np.where(rgb>0.04045,((rgb+0.0555)/1.0555)**2.4,rgb/12.92)

python/damask/_config.py

@@ -6,6 +6,9 @@ import abc
 import numpy as np
 import yaml
 
+from . import Rotation
+from . import Orientation
+
 class NiceDumper(yaml.SafeDumper):
     """Make YAML readable for humans."""
 
@@ -20,8 +23,12 @@ class NiceDumper(yaml.SafeDumper):
 
     def represent_data(self, data):
         """Cast Config objects and its subclasses to dict."""
-        return self.represent_data(dict(data)) if isinstance(data, dict) and type(data) != dict else \
+        if isinstance(data, dict) and type(data) != dict:
-               super().represent_data(data)
+            return self.represent_data(dict(data))
+        if isinstance(data, (Rotation, Orientation)):
+            return self.represent_data(data.as_quaternion())
+        else:
+            return super().represent_data(data)
 
     def ignore_aliases(self, data):
         """No references."""

python/damask/_configmaterial.py

@@ -1,4 +1,7 @@
+import os.path
+
 import numpy as np
+import h5py
 
 from . import Config
 from . import Rotation
@@ -49,7 +52,7 @@ class ConfigMaterial(Config):
     @staticmethod
     def from_table(table,**kwargs):
         """
-        Load from an ASCII table.
+        Generate from an ASCII table.
 
         Parameters
         ----------
@@ -94,6 +97,79 @@ class ConfigMaterial(Config):
         return ConfigMaterial().material_add(**kwargs_)
 
 
+    @staticmethod
+    def load_DREAM3D(fname,
+                     grain_data=None,cell_data=None,cell_ensemble_data='CellEnsembleData',
+                     phases='Phases',Euler_angles='EulerAngles',phase_names='PhaseName',
+                     base_group=None):
+        """
+        Load DREAM.3D (HDF5) file.
+
+        Data in DREAM.3D files can be stored per cell ('CellData')
+        and/or per grain ('Grain Data'). Per default, cell-wise data
+        is assumed.
+
+        damask.Grid.load_DREAM3D allows to get the corresponding geometry
+        for the grid solver.
+
+        Parameters
+        ----------
+        fname : str
+            Filename of the DREAM.3D (HDF5) file.
+        grain_data : str
+            Name of the group (folder) containing grain-wise data. Defaults
+            to None, in which case cell-wise data is used.
+        cell_data : str
+            Name of the group (folder) containing cell-wise data. Defaults to
+            None in wich case it is automatically detected.
+        cell_ensemble_data : str
+            Name of the group (folder) containing data of cell ensembles. This
+            group is used to inquire the name of the phases. Phases will get
+            numeric IDs if this group is not found. Defaults to 'CellEnsembleData'.
+        phases : str
+            Name of the dataset containing the phase ID (cell-wise or grain-wise).
+            Defaults to 'Phases'.
+        Euler_angles : str
+            Name of the dataset containing the crystallographic orientation as
+            Euler angles in radians (cell-wise or grain-wise). Defaults to 'EulerAngles'.
+        phase_names : str
+            Name of the dataset containing the phase names. Phases will get
+            numeric IDs if this dataset is not found. Defaults to 'PhaseName'.
+        base_group : str
+            Path to the group (folder) that contains geometry (_SIMPL_GEOMETRY),
+            and grain- or cell-wise data. Defaults to None, in which case
+            it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
+
+        """
+        b = util.DREAM3D_base_group(fname) if base_group is None else base_group
+        c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
+        f = h5py.File(fname,'r')
+
+        if grain_data is None:
+            phase = f[os.path.join(b,c,phases)][()].flatten()
+            O = Rotation.from_Euler_angles(f[os.path.join(b,c,Euler_angles)]).as_quaternion().reshape(-1,4) # noqa
+            _,idx = np.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0)
+            idx = np.sort(idx)
+        else:
+            phase = f[os.path.join(b,grain_data,phases)][()]
+            O = Rotation.from_Euler_angles(f[os.path.join(b,grain_data,Euler_angles)]).as_quaternion() # noqa
+            idx = np.arange(phase.size)
+
+        if cell_ensemble_data is not None and phase_names is not None:
+            try:
+                names = np.array([s.decode() for s in f[os.path.join(b,cell_ensemble_data,phase_names)]])
+                phase = names[phase]
+            except KeyError:
+                pass
+
+
+        base_config = ConfigMaterial({'phase':{k if isinstance(k,int) else str(k):'t.b.d.' for k in np.unique(phase)},
+                                      'homogenization':{'direct':{'N_constituents':1}}})
+        constituent = {k:np.atleast_1d(v[idx].squeeze()) for k,v in zip(['O','phase'],[O,phase])}
+
+        return base_config.material_add(**constituent,homogenization='direct')
+
+
     @property
     def is_complete(self):
         """Check for completeness."""

python/damask/_grid.py

@@ -256,35 +256,62 @@ class Grid:
 
 
     @staticmethod
-    def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
+    def load_DREAM3D(fname,
+                     feature_IDs=None,cell_data=None,
+                     phases='Phases',Euler_angles='EulerAngles',
+                     base_group=None):
         """
-        Load from DREAM.3D file.
+        Load DREAM.3D (HDF5) file.
+
+        Data in DREAM.3D files can be stored per cell ('CellData')
+        and/or per grain ('Grain Data'). Per default, cell-wise data
+        is assumed.
+
+        damask.ConfigMaterial.load_DREAM3D allows to get the
+        corresponding material definition.
 
         Parameters
         ----------
         fname : str
-            Filename of the DREAM.3D file
+            Filename of the DREAM.3D (HDF5) file.
+        feature_IDs : str
+            Name of the dataset containing the mapping between cells and
+            grain-wise data. Defaults to 'None', in which case cell-wise
+            data is used.
+        cell_data : str
+            Name of the group (folder) containing cell-wise data. Defaults to
+            None in wich case it is automatically detected.
+        phases : str
+            Name of the dataset containing the phase ID. It is not used for
+            grain-wise data, i.e. when feature_IDs is not None.
+            Defaults to 'Phases'.
+        Euler_angles : str
+            Name of the dataset containing the crystallographic orientation as
+            Euler angles in radians It is not used for grain-wise data, i.e.
+            when feature_IDs is not None. Defaults to 'EulerAngles'.
         base_group : str
-            Name of the group (folder) below 'DataContainers',
+            Path to the group (folder) that contains geometry (_SIMPL_GEOMETRY),
-            for example 'SyntheticVolumeDataContainer'.
+            and grain- or cell-wise data. Defaults to None, in which case
-        point_data : str, optional
+            it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
-            Name of the group (folder) containing the pointwise material data,
+
-            for example 'CellData'. Defaults to None, in which case points are consecutively numbered.
-        material : str, optional
-            Name of the dataset containing the material ID.
-            Defaults to 'FeatureIds'.
 
         """
-        root_dir ='DataContainers'
+        b = util.DREAM3D_base_group(fname) if base_group is None else base_group
+        c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
         f = h5py.File(fname, 'r')
-        g = os.path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
-        cells  = f[os.path.join(g,'DIMENSIONS')][()]
-        size   = f[os.path.join(g,'SPACING')][()] * cells
-        origin = f[os.path.join(g,'ORIGIN')][()]
 
-        ma = np.arange(cells.prod(),dtype=int) \
+        cells  = f[os.path.join(b,'_SIMPL_GEOMETRY','DIMENSIONS')][()]
-             if point_data is None else \
+        size   = f[os.path.join(b,'_SIMPL_GEOMETRY','SPACING')] * cells
-             np.reshape(f[os.path.join(root_dir,base_group,point_data,material)],cells.prod())
+        origin = f[os.path.join(b,'_SIMPL_GEOMETRY','ORIGIN')][()]
+
+        if feature_IDs is None:
+            phase = f[os.path.join(b,c,phases)][()].reshape(-1,1)
+            O = Rotation.from_Euler_angles(f[os.path.join(b,c,Euler_angles)]).as_quaternion().reshape(-1,4) # noqa
+            unique,unique_inverse = np.unique(np.hstack([O,phase]),return_inverse=True,axis=0)
+            ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
+                 np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
+        else:
+            ma = f[os.path.join(b,c,feature_IDs)][()].flatten()
 
         return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','load_DREAM3D'))
 
@@ -482,18 +509,13 @@ class Grid:
 
         References
         ----------
-        Sébastien B G Blanquer, Maike Werner, Markus Hannula, Shahriar Sharifi,
+        S.B.G. Blanquer et al., Biofabrication 9(2):025001, 2017
-        Guillaume P R Lajoinie, David Eglin, Jari Hyttinen, André A Poot, and Dirk W Grijpma
-        Surface curvature in triply-periodic minimal surface architectures as
-        a distinct design parameter in preparing advanced tissue engineering scaffolds
         https://doi.org/10.1088/1758-5090/aa6553
 
-        Meinhard Wohlgemuth, Nataliya Yufa, James Hoffman, and Edwin L. Thomas
+        M. Wohlgemuth et al., Macromolecules 34(17):6083-6089, 2001
-        Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
         https://doi.org/10.1021/ma0019499
 
-        Meng-Ting Hsieh, Lorenzo Valdevit
+        M.-T. Hsieh and L. Valdevit, Software Impacts 6:100026, 2020
-        Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
         https://doi.org/10.1016/j.simpa.2020.100026
 
         """

python/damask/_orientation.py

@@ -742,8 +742,7 @@ class Orientation(Rotation):
 
         References
         ----------
-        C.T. Young and J.L. Lytton, J. Appl. Phys. 43:1408–1417, 1972
+        C.T. Young and J.L. Lytton, Journal of Applied Physics 43:1408–1417, 1972
-        "Computer Generation and Identification of Kikuchi Projections"
         https://doi.org/10.1063/1.1661333
 
         """
@@ -1070,8 +1069,7 @@ class Orientation(Rotation):
 
         References
         ----------
-        J.C. Glez and J. Driver, J. Appl. Cryst. 34:280-288, 2001
+        J.C. Glez and J. Driver, Journal of Applied Crystallography 34:280-288, 2001
-        "Orientation distribution analysis in deformed grains"
         https://doi.org/10.1107/S0021889801003077
 
         """

python/damask/_result.py

@@ -46,7 +46,7 @@ class Result:
             self.version_major = f.attrs['DADF5_version_major']
             self.version_minor = f.attrs['DADF5_version_minor']
 
-            if self.version_major != 0 or not 7 <= self.version_minor <= 11:
+            if self.version_major != 0 or not 7 <= self.version_minor <= 12:
                 raise TypeError(f'Unsupported DADF5 version {self.version_major}.{self.version_minor}')
 
             self.structured = 'grid' in f['geometry'].attrs.keys() or \
@@ -60,15 +60,20 @@ class Result:
                 self.size   = f['geometry'].attrs['size']
                 self.origin = f['geometry'].attrs['origin']
 
-            r=re.compile('inc[0-9]+')
+            r=re.compile('inc[0-9]+' if self.version_minor < 12 else 'increment_[0-9]+')
-            increments_unsorted = {int(i[3:]):i for i in f.keys() if r.match(i)}
+            increments_unsorted = {int(i[10:]):i for i in f.keys() if r.match(i)}
             self.increments     = [increments_unsorted[i] for i in sorted(increments_unsorted)]
-            self.times          = [round(f[i].attrs['time/s'],12) for i in self.increments]
+            self.times          = [round(f[i].attrs['time/s'],12) for i in self.increments] if self.version_minor < 12 else \
+                                  [round(f[i].attrs['t/s'],12) for i in self.increments]
 
-            self.N_materialpoints, self.N_constituents = np.shape(f['mapping/phase'])
+            grp = 'mapping' if self.version_minor < 12 else 'cell_to'
 
-            self.homogenizations  = [m.decode() for m in np.unique(f['mapping/homogenization']['Name'])]
+            self.N_materialpoints, self.N_constituents = np.shape(f[f'{grp}/phase'])
-            self.phases           = [c.decode() for c in np.unique(f['mapping/phase']['Name'])]
+
+            self.homogenizations  = [m.decode() for m in np.unique(f[f'{grp}/homogenization']
+                                                                    ['Name' if self.version_minor < 12 else 'label'])]
+            self.phases           = [c.decode() for c in np.unique(f[f'{grp}/phase']
+                                                                    ['Name' if self.version_minor < 12 else 'label'])]
 
             self.out_type_ph = []
             for c in self.phases:
@@ -137,9 +142,10 @@ class Result:
         choice = datasets if hasattr(datasets,'__iter__') and not isinstance(datasets,str) else \
                 [datasets]
 
+        inc = 'inc' if self.version_minor < 12 else 'increment_' # compatibility hack
         if   what == 'increments':
-            choice = [c if isinstance(c,str) and c.startswith('inc') else
+            choice = [c if isinstance(c,str) and c.startswith(inc) else
-                      f'inc{c}' for c in choice]
+                      f'{inc}{c}' for c in choice]
         elif what == 'times':
             what = 'increments'
             if choice == ['*']:
@@ -204,7 +210,7 @@ class Result:
         self._allow_modification = False
 
 
-    def incs_in_range(self,start,end):
+    def increments_in_range(self,start,end):
         """
         Select all increments within a given range.
 
@@ -216,9 +222,11 @@ class Result:
             End increment.
 
         """
+        # compatibility hack
+        ln = 3 if self.version_minor < 12 else 10
         selected = []
-        for i,inc in enumerate([int(i[3:]) for i in self.increments]):
+        for i,inc in enumerate([int(i[ln:]) for i in self.increments]):
-            s,e = map(lambda x: int(x[3:] if isinstance(x,str) and x.startswith('inc') else x), (start,end))
+            s,e = map(lambda x: int(x[ln:] if isinstance(x,str) and x.startswith('inc') else x), (start,end))
             if s <= inc <= e:
                 selected.append(self.increments[i])
         return selected
@@ -368,6 +376,10 @@ class Result:
         tbl = {} if split else None
         inGeom = {}
         inData = {}
+        # compatibility hack
+        name   = 'Name' if self.version_minor < 12 else 'label'
+        member = 'Position' if self.version_minor < 12 else 'entry'
+        grp    = 'mapping' if self.version_minor < 12 else 'cell_to'
         with h5py.File(self.fname,'r') as f:
             for dataset in sets:
                 for group in self.groups_with_datasets(dataset):
@@ -378,11 +390,11 @@ class Result:
                         if prop == 'geometry':
                             inGeom[key] = inData[key] = np.arange(self.N_materialpoints)
                         elif prop == 'phase':
-                            inGeom[key] = np.where(f['mapping/phase'][:,constituent]['Name'] == str.encode(name))[0]
+                            inGeom[key] = np.where(f[f'{grp}/phase'][:,constituent][name] == str.encode(name))[0]
-                            inData[key] =          f['mapping/phase'][inGeom[key],constituent]['Position']
+                            inData[key] =          f[f'{grp}/phase'][inGeom[key],constituent][member]
                         elif prop == 'homogenization':
-                            inGeom[key] = np.where(f['mapping/homogenization']['Name'] == str.encode(name))[0]
+                            inGeom[key] = np.where(f[f'{grp}/homogenization'][name] == str.encode(name))[0]
-                            inData[key] =          f['mapping/homogenization'][inGeom[key].tolist()]['Position']
+                            inData[key] =          f[f'{grp}/homogenization'][inGeom[key].tolist()][member]
                     shape = np.shape(f[path])
                     data = np.full((self.N_materialpoints,) + (shape[1:] if len(shape)>1 else (1,)),
                                    np.nan,
@@ -456,6 +468,9 @@ class Result:
 
     def list_data(self):
         """Return information on all active datasets in the file."""
+        # compatibility hack
+        de = 'Description' if self.version_minor < 12 else 'description'
+        un = 'Unit'        if self.version_minor < 12 else 'unit'
         message = ''
         with h5py.File(self.fname,'r') as f:
             for i in self.iterate('increments'):
@@ -470,13 +485,13 @@ class Result:
                             for d in f[group].keys():
                                 try:
                                     dataset = f['/'.join([group,d])]
-                                    if 'Unit' in dataset.attrs:
+                                    if un in dataset.attrs:
-                                        unit = f" / {dataset.attrs['Unit']}" if h5py3 else \
+                                        unit = f" / {dataset.attrs[un]}" if h5py3 else \
-                                               f" / {dataset.attrs['Unit'].decode()}"
+                                               f" / {dataset.attrs[un].decode()}"
                                     else:
                                         unit = ''
-                                    description = dataset.attrs['Description'] if h5py3 else \
+                                    description = dataset.attrs[de] if h5py3 else \
-                                                  dataset.attrs['Description'].decode()
+                                                  dataset.attrs[de].decode()
                                     message += f'        {d}{unit}: {description}\n'
                                 except KeyError:
                                     pass
@@ -529,6 +544,10 @@ class Result:
             Defaults to False.
 
         """
+        # compatibility hack
+        name   = 'Name' if self.version_minor < 12 else 'label'
+        member = 'Position' if self.version_minor < 12 else 'entry'
+        grp    = 'mapping' if self.version_minor < 12 else 'cell_to'
         with h5py.File(self.fname,'r') as f:
             shape = (self.N_materialpoints,) + np.shape(f[path[0]])[1:]
             if len(shape) == 1: shape = shape +(1,)
@@ -540,17 +559,17 @@ class Result:
                     dataset = np.array(f[pa])
                     continue
 
-                p = np.where(f['mapping/phase'][:,c]['Name'] == str.encode(label))[0]
+                p = np.where(f[f'{grp}/phase'][:,c][name] == str.encode(label))[0]
                 if len(p)>0:
-                    u = (f['mapping/phase']['Position'][p,c])
+                    u = (f[f'{grp}/phase'][member][p,c])
                     a = np.array(f[pa])
                     if len(a.shape) == 1:
                         a=a.reshape([a.shape[0],1])
                     dataset[p,:] = a[u,:]
 
-                p = np.where(f['mapping/homogenization']['Name'] == str.encode(label))[0]
+                p = np.where(f[f'{grp}/homogenization'][name] == str.encode(label))[0]
                 if len(p)>0:
-                    u = (f['mapping/homogenization']['Position'][p.tolist()])
+                    u = (f[f'{grp}/homogenization'][member][p.tolist()])
                     a = np.array(f[pa])
                     if len(a.shape) == 1:
                         a=a.reshape([a.shape[0],1])
@@ -586,9 +605,9 @@ class Result:
                 'data':  np.abs(x['data']),
                 'label': f'|{x["label"]}|',
                 'meta':  {
-                          'Unit':        x['meta']['Unit'],
+                          'unit':        x['meta']['unit'],
-                          'Description': f"Absolute value of {x['label']} ({x['meta']['Description']})",
+                          'description': f"absolute value of {x['label']} ({x['meta']['description']})",
-                          'Creator':     'add_absolute'
+                          'creator':     'add_absolute'
                           }
                  }
     def add_absolute(self,x):
@@ -614,9 +633,9 @@ class Result:
                 'data':  eval(formula),
                 'label': kwargs['label'],
                 'meta':  {
-                          'Unit':        kwargs['unit'],
+                          'unit':        kwargs['unit'],
-                          'Description': f"{kwargs['description']} (formula: {kwargs['formula']})",
+                          'description': f"{kwargs['description']} (formula: {kwargs['formula']})",
-                          'Creator':     'add_calculation'
+                          'creator':     'add_calculation'
                           }
                  }
     def add_calculation(self,label,formula,unit='n/a',description=None):
@@ -646,11 +665,11 @@ class Result:
                 'data':  mechanics.stress_Cauchy(P['data'],F['data']),
                 'label': 'sigma',
                 'meta':  {
-                          'Unit':        P['meta']['Unit'],
+                          'unit':        P['meta']['unit'],
-                          'Description': "Cauchy stress calculated "
+                          'description': "Cauchy stress calculated "
-                                         f"from {P['label']} ({P['meta']['Description']})"
+                                         f"from {P['label']} ({P['meta']['description']})"
-                                         f" and {F['label']} ({F['meta']['Description']})",
+                                         f" and {F['label']} ({F['meta']['description']})",
-                          'Creator':     'add_stress_Cauchy'
+                          'creator':     'add_stress_Cauchy'
                           }
                 }
     def add_stress_Cauchy(self,P='P',F='F'):
@@ -674,9 +693,9 @@ class Result:
                 'data':  np.linalg.det(T['data']),
                 'label': f"det({T['label']})",
                 'meta':  {
-                          'Unit':        T['meta']['Unit'],
+                          'unit':        T['meta']['unit'],
-                          'Description': f"Determinant of tensor {T['label']} ({T['meta']['Description']})",
+                          'description': f"determinant of tensor {T['label']} ({T['meta']['description']})",
-                          'Creator':     'add_determinant'
+                          'creator':     'add_determinant'
                           }
                 }
     def add_determinant(self,T):
@@ -698,9 +717,9 @@ class Result:
                 'data':  tensor.deviatoric(T['data']),
                 'label': f"s_{T['label']}",
                 'meta':  {
-                          'Unit':        T['meta']['Unit'],
+                          'unit':        T['meta']['unit'],
-                          'Description': f"Deviator of tensor {T['label']} ({T['meta']['Description']})",
+                          'description': f"deviator of tensor {T['label']} ({T['meta']['description']})",
-                          'Creator':     'add_deviator'
+                          'creator':     'add_deviator'
                           }
                  }
     def add_deviator(self,T):
@@ -719,19 +738,19 @@ class Result:
     @staticmethod
     def _add_eigenvalue(T_sym,eigenvalue):
         if   eigenvalue == 'max':
-            label,p = 'Maximum',2
+            label,p = 'maximum',2
         elif eigenvalue == 'mid':
-            label,p = 'Intermediate',1
+            label,p = 'intermediate',1
         elif eigenvalue == 'min':
-            label,p = 'Minimum',0
+            label,p = 'minimum',0
 
         return {
                 'data': tensor.eigenvalues(T_sym['data'])[:,p],
                 'label': f"lambda_{eigenvalue}({T_sym['label']})",
                 'meta' : {
-                          'Unit':         T_sym['meta']['Unit'],
+                          'unit':        T_sym['meta']['unit'],
-                          'Description': f"{label} eigenvalue of {T_sym['label']} ({T_sym['meta']['Description']})",
+                          'description': f"{label} eigenvalue of {T_sym['label']} ({T_sym['meta']['description']})",
-                          'Creator':     'add_eigenvalue'
+                          'creator':     'add_eigenvalue'
                          }
                 }
     def add_eigenvalue(self,T_sym,eigenvalue='max'):
@@ -761,10 +780,10 @@ class Result:
                 'data': tensor.eigenvectors(T_sym['data'])[:,p],
                 'label': f"v_{eigenvalue}({T_sym['label']})",
                 'meta' : {
-                          'Unit':        '1',
+                          'unit':        '1',
-                          'Description': f"Eigenvector corresponding to {label} eigenvalue"
+                          'description': f"eigenvector corresponding to {label} eigenvalue"
-                                         f" of {T_sym['label']} ({T_sym['meta']['Description']})",
+                                         f" of {T_sym['label']} ({T_sym['meta']['description']})",
-                          'Creator':     'add_eigenvector'
+                          'creator':     'add_eigenvector'
                          }
                }
     def add_eigenvector(self,T_sym,eigenvalue='max'):
@@ -787,9 +806,9 @@ class Result:
     def _add_IPF_color(l,q):
         m = util.scale_to_coprime(np.array(l))
         try:
-            lattice = {'fcc':'cF','bcc':'cI','hex':'hP'}[q['meta']['Lattice']]
+            lattice = {'fcc':'cF','bcc':'cI','hex':'hP'}[q['meta']['lattice']]
         except KeyError:
-            lattice =  q['meta']['Lattice']
+            lattice =  q['meta']['lattice']
         try:
             o = Orientation(rotation = (rfn.structured_to_unstructured(q['data'])),lattice=lattice)
         except ValueError:
@@ -799,10 +818,10 @@ class Result:
                 'data': np.uint8(o.IPF_color(l)*255),
                 'label': 'IPFcolor_[{} {} {}]'.format(*m),
                 'meta' : {
-                          'Unit':        '8-bit RGB',
+                          'unit':        '8-bit RGB',
-                          'Lattice':     q['meta']['Lattice'],
+                          'lattice':     q['meta']['lattice'],
-                          'Description': 'Inverse Pole Figure (IPF) colors along sample direction [{} {} {}]'.format(*m),
+                          'description': 'Inverse Pole Figure (IPF) colors along sample direction [{} {} {}]'.format(*m),
-                          'Creator':     'add_IPF_color'
+                          'creator':     'add_IPF_color'
                          }
                }
     def add_IPF_color(self,l,q='O'):
@@ -827,9 +846,9 @@ class Result:
                 'data':  mechanics.maximum_shear(T_sym['data']),
                 'label': f"max_shear({T_sym['label']})",
                 'meta':  {
-                          'Unit':        T_sym['meta']['Unit'],
+                          'unit':        T_sym['meta']['unit'],
-                          'Description': f"Maximum shear component of {T_sym['label']} ({T_sym['meta']['Description']})",
+                          'description': f"maximum shear component of {T_sym['label']} ({T_sym['meta']['description']})",
-                          'Creator':     'add_maximum_shear'
+                          'creator':     'add_maximum_shear'
                           }
                  }
     def add_maximum_shear(self,T_sym):
@@ -849,9 +868,9 @@ class Result:
     def _add_equivalent_Mises(T_sym,kind):
         k = kind
         if k is None:
-            if T_sym['meta']['Unit'] == '1':
+            if T_sym['meta']['unit'] == '1':
                 k = 'strain'
-            elif T_sym['meta']['Unit'] == 'Pa':
+            elif T_sym['meta']['unit'] == 'Pa':
                 k = 'stress'
         if k not in ['stress', 'strain']:
             raise ValueError('invalid von Mises kind {kind}')
@@ -861,9 +880,9 @@ class Result:
                           mechanics.equivalent_stress_Mises)(T_sym['data']),
                 'label': f"{T_sym['label']}_vM",
                 'meta':  {
-                          'Unit':        T_sym['meta']['Unit'],
+                          'unit':        T_sym['meta']['unit'],
-                          'Description': f"Mises equivalent {k} of {T_sym['label']} ({T_sym['meta']['Description']})",
+                          'description': f"Mises equivalent {k} of {T_sym['label']} ({T_sym['meta']['description']})",
-                          'Creator':     'add_Mises'
+                          'creator':     'add_Mises'
                           }
                 }
     def add_equivalent_Mises(self,T_sym,kind=None):
@@ -900,9 +919,9 @@ class Result:
                 'data':  np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True),
                 'label': f"|{x['label']}|_{o}",
                 'meta':  {
-                          'Unit':        x['meta']['Unit'],
+                          'unit':        x['meta']['unit'],
-                          'Description': f"{o}-norm of {t} {x['label']} ({x['meta']['Description']})",
+                          'description': f"{o}-norm of {t} {x['label']} ({x['meta']['description']})",
-                          'Creator':     'add_norm'
+                          'creator':     'add_norm'
                           }
                  }
     def add_norm(self,x,ord=None):
@@ -926,11 +945,11 @@ class Result:
                 'data':  mechanics.stress_second_Piola_Kirchhoff(P['data'],F['data']),
                 'label': 'S',
                 'meta':  {
-                          'Unit':        P['meta']['Unit'],
+                          'unit':        P['meta']['unit'],
-                          'Description': "2. Piola-Kirchhoff stress calculated "
+                          'description': "second Piola-Kirchhoff stress calculated "
-                                         f"from {P['label']} ({P['meta']['Description']})"
+                                         f"from {P['label']} ({P['meta']['description']})"
-                                         f" and {F['label']} ({F['meta']['Description']})",
+                                         f" and {F['label']} ({F['meta']['description']})",
-                          'Creator':     'add_stress_second_Piola_Kirchhoff'
+                          'creator':     'add_stress_second_Piola_Kirchhoff'
                           }
                 }
     def add_stress_second_Piola_Kirchhoff(self,P='P',F='F'):
@@ -968,10 +987,10 @@ class Result:
     #             'data': coords,
     #             'label': 'p^{}_[{} {} {})'.format(u'rφ' if polar else 'xy',*m),
     #             'meta' : {
-    #                       'Unit':        '1',
+    #                       'unit':        '1',
-    #                       'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\
+    #                       'description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\
     #                                      .format('Polar' if polar else 'Cartesian'),
-    #                       'Creator':     'add_pole'
+    #                       'creator':     'add_pole'
     #                      }
     #            }
     # def add_pole(self,q,p,polar=False):
@@ -997,9 +1016,9 @@ class Result:
                 'data':  mechanics.rotation(F['data']).as_matrix(),
                 'label': f"R({F['label']})",
                 'meta':  {
-                          'Unit':        F['meta']['Unit'],
+                          'unit':        F['meta']['unit'],
-                          'Description': f"Rotational part of {F['label']} ({F['meta']['Description']})",
+                          'description': f"rotational part of {F['label']} ({F['meta']['description']})",
-                          'Creator':     'add_rotation'
+                          'creator':     'add_rotation'
                           }
                  }
     def add_rotation(self,F):
@@ -1021,9 +1040,9 @@ class Result:
                 'data':  tensor.spherical(T['data'],False),
                 'label': f"p_{T['label']}",
                 'meta':  {
-                          'Unit':        T['meta']['Unit'],
+                          'unit':        T['meta']['unit'],
-                          'Description': f"Spherical component of tensor {T['label']} ({T['meta']['Description']})",
+                          'description': f"spherical component of tensor {T['label']} ({T['meta']['description']})",
-                          'Creator':     'add_spherical'
+                          'creator':     'add_spherical'
                           }
                  }
     def add_spherical(self,T):
@@ -1045,9 +1064,9 @@ class Result:
                 'data':  mechanics.strain(F['data'],t,m),
                 'label': f"epsilon_{t}^{m}({F['label']})",
                 'meta':  {
-                          'Unit':        F['meta']['Unit'],
+                          'unit':        F['meta']['unit'],
-                          'Description': f"Strain tensor of {F['label']} ({F['meta']['Description']})",
+                          'description': f"strain tensor of {F['label']} ({F['meta']['description']})",
-                          'Creator':     'add_strain'
+                          'creator':     'add_strain'
                           }
                  }
     def add_strain(self,F='F',t='V',m=0.0):
@@ -1076,10 +1095,10 @@ class Result:
                 'data':  (mechanics.stretch_left if t.upper() == 'V' else mechanics.stretch_right)(F['data']),
                 'label': f"{t}({F['label']})",
                 'meta':  {
-                          'Unit':        F['meta']['Unit'],
+                          'unit':        F['meta']['unit'],
-                          'Description': '{} stretch tensor of {} ({})'.format('Left' if t.upper() == 'V' else 'Right',
+                          'description': '{} stretch tensor of {} ({})'.format('left' if t.upper() == 'V' else 'right',
-                                                                               F['label'],F['meta']['Description']),
+                                                                               F['label'],F['meta']['description']),
-                          'Creator':     'add_stretch_tensor'
+                          'creator':     'add_stretch_tensor'
                           }
                  }
     def add_stretch_tensor(self,F='F',t='V'):
@@ -1153,8 +1172,7 @@ class Result:
                     if self._allow_modification and result[0]+'/'+result[1]['label'] in f:
                         dataset = f[result[0]+'/'+result[1]['label']]
                         dataset[...] = result[1]['data']
-                        dataset.attrs['Overwritten'] = 'Yes' if h5py3 else \
+                        dataset.attrs['overwritten'] = True
-                                                       'Yes'.encode()
                     else:
                         if result[1]['data'].size >= chunk_size*2:
                             shape  = result[1]['data'].shape
@@ -1167,14 +1185,14 @@ class Result:
                             dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data'])
 
                     now = datetime.datetime.now().astimezone()
-                    dataset.attrs['Created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \
+                    dataset.attrs['created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \
                                                now.strftime('%Y-%m-%d %H:%M:%S%z').encode()
 
                     for l,v in result[1]['meta'].items():
-                        dataset.attrs[l]=v if h5py3 else v.encode()
+                        dataset.attrs[l.lower()]=v if h5py3 else v.encode()
-                    creator = dataset.attrs['Creator'] if h5py3 else \
+                    creator = dataset.attrs['creator'] if h5py3 else \
-                              dataset.attrs['Creator'].decode()
+                              dataset.attrs['creator'].decode()
-                    dataset.attrs['Creator'] = f"damask.Result.{creator} v{damask.version}" if h5py3 else \
+                    dataset.attrs['creator'] = f"damask.Result.{creator} v{damask.version}" if h5py3 else \
                                                f"damask.Result.{creator} v{damask.version}".encode()
 
                 except (OSError,RuntimeError) as err:
@@ -1192,6 +1210,8 @@ class Result:
         The view is not taken into account, i.e. the content of the
         whole file will be included.
         """
+        # compatibility hack
+        u = 'Unit' if self.version_minor < 12 else 'unit'
         if self.N_constituents != 1 or len(self.phases) != 1 or not self.structured:
             raise TypeError('XDMF output requires homogeneous grid')
 
@@ -1273,7 +1293,7 @@ class Result:
                                 dtype = f[name].dtype
 
                                 if dtype not in np.sctypes['int']+np.sctypes['uint']+np.sctypes['float']: continue
-                                unit = f[name].attrs['Unit'] if h5py3 else f[name].attrs['Unit'].decode()
+                                unit = f[name].attrs[u] if h5py3 else f[name].attrs[u].decode()
 
                                 attributes.append(ET.SubElement(grid, 'Attribute'))
                                 attributes[-1].attrib={'Name':          name.split('/',2)[2]+f' / {unit}',
@@ -1317,7 +1337,10 @@ class Result:
         elif mode.lower()=='point':
             v = VTK.from_poly_data(self.coordinates0_point)
 
-        N_digits = int(np.floor(np.log10(max(1,int(self.increments[-1][3:])))))+1
+        # compatibility hack
+        ln = 3 if self.version_minor < 12 else 10
+
+        N_digits = int(np.floor(np.log10(max(1,int(self.increments[-1][ln:])))))+1
 
         for inc in util.show_progress(self.iterate('increments'),len(self.visible['increments'])):
 
@@ -1327,21 +1350,24 @@ class Result:
                 for o in self.iterate('out_type_ph'):
                     for c in range(self.N_constituents):
                         prefix = '' if self.N_constituents == 1 else f'constituent{c}/'
-                        if o != 'mechanics':
+                        if o not in ['mechanics', 'mechanical']:                                    # compatibility hack
                             for _ in self.iterate('phases'):
                                 path = self.get_dataset_location(label)
                                 if len(path) == 0:
                                     continue
                                 array = self.read_dataset(path,c)
-                                v.add(array,prefix+path[0].split('/',1)[1]+f' / {self._get_attribute(path[0],"Unit")}')
+                                v.add(array,prefix+path[0].split('/',1)[1]+f' / {self._get_attribute(path[0],"unit")}')
                         else:
                             paths = self.get_dataset_location(label)
                             if len(paths) == 0:
                                 continue
                             array = self.read_dataset(paths,c)
+                            if self.version_minor < 12:
                                 ph_name = re.compile(r'(?<=(phase\/))(.*?)(?=(mechanics))')         # identify  phase name
+                            else:
+                                ph_name = re.compile(r'(?<=(phase\/))(.*?)(?=(mechanical))')        # identify  phase name
                             dset_name = prefix+re.sub(ph_name,r'',paths[0].split('/',1)[1])         # remove phase name
-                            v.add(array,dset_name+f' / {self._get_attribute(paths[0],"Unit")}')
+                            v.add(array,dset_name+f' / {self._get_attribute(paths[0],"unit")}')
             self.view('homogenizations',viewed_backup_ho)
 
             viewed_backup_ph = self.visible['phases'].copy()
@@ -1352,10 +1378,10 @@ class Result:
                     if len(paths) == 0:
                         continue
                     array = self.read_dataset(paths)
-                    v.add(array,paths[0].split('/',1)[1]+f' / {self._get_attribute(paths[0],"Unit")}')
+                    v.add(array,paths[0].split('/',1)[1]+f' / {self._get_attribute(paths[0],"unit")}')
             self.view('phases',viewed_backup_ph)
 
             u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
             v.add(u,'u')
 
-            v.save(f'{self.fname.stem}_inc{inc[3:].zfill(N_digits)}')
+            v.save(f'{self.fname.stem}_inc{inc[ln:].zfill(N_digits)}')

python/damask/_rotation.py

@@ -357,10 +357,8 @@ class Rotation:
 
         References
         ----------
-        Quaternion averaging
+        F. Landis Markley et al., Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
-        F. Landis Markley, Yang Cheng, John L. Crassidis, Yaakov Oshman
+        https://doi.org/10.2514/1.28949
-        Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
-        10.2514/1.28949
 
         """
         def _M(quat):
@@ -859,7 +857,7 @@ class Rotation:
 
         References
         ----------
-        P. Eisenlohr, F. Roters, Computational Materials Science 42(4), 670-678, 2008
+        P. Eisenlohr and F. Roters, Computational Materials Science 42(4):670-678, 2008
         https://doi.org/10.1016/j.commatsci.2007.09.015
 
         """

python/damask/util.py

@@ -9,6 +9,7 @@ from functools import reduce
 from optparse import Option
 
 import numpy as np
+import h5py
 
 from . import version
 
@@ -27,7 +28,8 @@ __all__=[
          'extendableOption',
          'execution_stamp',
          'shapeshifter', 'shapeblender',
-         'extend_docstring', 'extended_docstring'
+         'extend_docstring', 'extended_docstring',
+         'DREAM3D_base_group', 'DREAM3D_cell_data_group'
         ]
 
 ####################################################################################################
@@ -376,6 +378,53 @@ def extended_docstring(f,extra_docstring):
     return _decorator
 
 
+def DREAM3D_base_group(fname):
+    """
+    Determine the base group of a DREAM.3D file.
+
+    The base group is defined as the group (folder) that contains
+    a 'SPACING' dataset in a '_SIMPL_GEOMETRY' group.
+
+    Parameters
+    ----------
+    fname : str
+        Filename of the DREAM.3D (HDF5) file.
+
+    """
+    with h5py.File(fname,'r') as f:
+        base_group = f.visit(lambda path: path.rsplit('/',2)[0] if '_SIMPL_GEOMETRY/SPACING' in path else None)
+
+    if base_group is None:
+        raise ValueError(f'Could not determine base group in file {fname}.')
+
+    return base_group
+
+def DREAM3D_cell_data_group(fname):
+    """
+    Determine the cell data group of a DREAM.3D file.
+
+    The cell data group is defined as the group (folder) that contains
+    a dataset in the base group whose length matches the total number
+    of points as specified in '_SIMPL_GEOMETRY/DIMENSIONS'.
+
+    Parameters
+    ----------
+    fname : str
+        Filename of the DREAM.3D (HDF5) file.
+
+    """
+    base_group = DREAM3D_base_group(fname)
+    with h5py.File(fname,'r') as f:
+        cells = tuple(f[os.path.join(base_group,'_SIMPL_GEOMETRY','DIMENSIONS')][()][::-1])
+        cell_data_group = f[base_group].visititems(lambda path,obj: path.split('/')[0] \
+                                                   if isinstance(obj,h5py._hl.dataset.Dataset) and np.shape(obj)[:-1] == cells \
+                                                   else None)
+
+    if cell_data_group is None:
+        raise ValueError(f'Could not determine cell data group in file {fname}/{base_group}.')
+
+    return cell_data_group
+
 ####################################################################################################
 # Classes
 ####################################################################################################

python/tests/reference/ConfigMaterial/2phase_irregularGrid.dream3d

@@ -0,0 +1 @@
+../Grid/2phase_irregularGrid.dream3d

python/tests/reference/ConfigMaterial/2phase_irregularGrid.json

@@ -0,0 +1 @@
+../Grid/2phase_irregularGrid.json

python/tests/reference/ConfigMaterial/2phase_irregularGrid.xdmf

@@ -0,0 +1 @@
+../Grid/2phase_irregularGrid.xdmf

python/tests/reference/ConfigMaterial/measured.dream3d

@@ -0,0 +1 @@
+../Grid/measured.dream3d

python/tests/reference/ConfigMaterial/measured.xdmf

@@ -0,0 +1 @@
+../Grid/measured.xdmf

python/tests/reference/Grid/2phase_irregularGrid.json

@@ -0,0 +1,764 @@
+{
+    "0": {
+        "CellEnsembleAttributeMatrixName": "CellEnsembleData",
+        "CrystalStructuresArrayName": "CrystalStructures",
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+        "Filter_Name": "StatsGeneratorFilter",
+        "Filter_Uuid": "{f642e217-4722-5dd8-9df9-cee71e7b26ba}",
+        "PhaseNamesArrayName": "PhaseName",
+        "PhaseTypesArrayName": "PhaseTypes",
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+        "InputStatsArrayPath": {
+            "Attribute Matrix Name": "CellEnsembleData",
+            "Data Array Name": "Statistics",
+            "Data Container Name": "StatsGeneratorDataContainer"
+        },
+        "MaskArrayPath": {
+            "Attribute Matrix Name": "",
+            "Data Array Name": "",
+            "Data Container Name": ""
+        },
+        "NewAttributeMatrixPath": {
+            "Attribute Matrix Name": "Synthetic Shape Parameters (Primary Phase)",
+            "Data Array Name": "",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "NumFeaturesArrayName": "NumFeatures",
+        "OutputCellAttributeMatrixPath": {
+            "Attribute Matrix Name": "CellData",
+            "Data Array Name": "",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "OutputCellEnsembleAttributeMatrixName": "CellEnsembleData",
+        "OutputCellFeatureAttributeMatrixName": "Grain Data",
+        "PeriodicBoundaries": 0,
+        "SaveGeometricDescriptions": 0,
+        "SelectedAttributeMatrixPath": {
+            "Attribute Matrix Name": "",
+            "Data Array Name": "",
+            "Data Container Name": ""
+        },
+        "UseMask": 0
+    },
+    "4": {
+        "BoundaryCellsArrayName": "BoundaryCells",
+        "FeatureIdsArrayPath": {
+            "Attribute Matrix Name": "CellData",
+            "Data Array Name": "FeatureIds",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "FilterVersion": "6.5.138",
+        "Filter_Enabled": true,
+        "Filter_Human_Label": "Find Boundary Cells (Image)",
+        "Filter_Name": "FindBoundaryCells",
+        "Filter_Uuid": "{8a1106d4-c67f-5e09-a02a-b2e9b99d031e}",
+        "IgnoreFeatureZero": 1,
+        "IncludeVolumeBoundary": 0
+    },
+    "5": {
+        "BoundaryCellsArrayPath": {
+            "Attribute Matrix Name": "CellData",
+            "Data Array Name": "BoundaryCells",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "CellPhasesArrayPath": {
+            "Attribute Matrix Name": "CellData",
+            "Data Array Name": "Phases",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "FeatureGeneration": 0,
+        "FeatureIdsArrayPath": {
+            "Attribute Matrix Name": "CellData",
+            "Data Array Name": "FeatureIds",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "FeaturePhasesArrayPath": {
+            "Attribute Matrix Name": "Grain Data",
+            "Data Array Name": "Phases",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "FilterVersion": "6.5.138",
+        "Filter_Enabled": true,
+        "Filter_Human_Label": "Insert Precipitate Phases",
+        "Filter_Name": "InsertPrecipitatePhases",
+        "Filter_Uuid": "{1e552e0c-53bb-5ae1-bd1c-c7a6590f9328}",
+        "InputPhaseTypesArrayPath": {
+            "Attribute Matrix Name": "CellEnsembleData",
+            "Data Array Name": "PhaseTypes",
+            "Data Container Name": "StatsGeneratorDataContainer"
+        },
+        "InputShapeTypesArrayPath": {
+            "Attribute Matrix Name": "CellEnsembleData",
+            "Data Array Name": "ShapeTypes",
+            "Data Container Name": "StatsGeneratorDataContainer"
+        },
+        "InputStatsArrayPath": {
+            "Attribute Matrix Name": "CellEnsembleData",
+            "Data Array Name": "Statistics",
+            "Data Container Name": "StatsGeneratorDataContainer"
+        },
+        "MaskArrayPath": {
+            "Attribute Matrix Name": "",
+            "Data Array Name": "",
+            "Data Container Name": ""
+        },
+        "MatchRDF": 0,
+        "NewAttributeMatrixPath": {
+            "Attribute Matrix Name": "Synthetic Shape Parameters (Precipitate)",
+            "Data Array Name": "",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "NumFeaturesArrayPath": {
+            "Attribute Matrix Name": "CellEnsembleData",
+            "Data Array Name": "NumFeatures",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "PeriodicBoundaries": 0,
+        "PrecipInputFile": "C:/Users/work",
+        "SaveGeometricDescriptions": 0,
+        "SelectedAttributeMatrixPath": {
+            "Attribute Matrix Name": "",
+            "Data Array Name": "",
+            "Data Container Name": ""
+        },
+        "UseMask": 0
+    },
+    "6": {
+        "BoundaryCellsArrayName": "BoundaryCells",
+        "CellFeatureAttributeMatrixPath": {
+            "Attribute Matrix Name": "Grain Data",
+            "Data Array Name": "",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "FeatureIdsArrayPath": {
+            "Attribute Matrix Name": "CellData",
+            "Data Array Name": "FeatureIds",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "FilterVersion": "6.5.138",
+        "Filter_Enabled": true,
+        "Filter_Human_Label": "Find Feature Neighbors",
+        "Filter_Name": "FindNeighbors",
+        "Filter_Uuid": "{97cf66f8-7a9b-5ec2-83eb-f8c4c8a17bac}",
+        "NeighborListArrayName": "NeighborList",
+        "NumNeighborsArrayName": "NumNeighbors",
+        "SharedSurfaceAreaListArrayName": "SharedSurfaceAreaList",
+        "StoreBoundaryCells": 0,
+        "StoreSurfaceFeatures": 1,
+        "SurfaceFeaturesArrayName": "SurfaceFeatures"
+    },
+    "7": {
+        "AvgQuatsArrayName": "AvgQuats",
+        "CellEulerAnglesArrayName": "EulerAngles",
+        "CrystalStructuresArrayPath": {
+            "Attribute Matrix Name": "CellEnsembleData",
+            "Data Array Name": "CrystalStructures",
+            "Data Container Name": "StatsGeneratorDataContainer"
+        },
+        "FeatureEulerAnglesArrayName": "EulerAngles",
+        "FeatureIdsArrayPath": {
+            "Attribute Matrix Name": "CellData",
+            "Data Array Name": "FeatureIds",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "FeaturePhasesArrayPath": {
+            "Attribute Matrix Name": "Grain Data",
+            "Data Array Name": "Phases",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "FilterVersion": "6.5.138",
+        "Filter_Enabled": true,
+        "Filter_Human_Label": "Match Crystallography",
+        "Filter_Name": "MatchCrystallography",
+        "Filter_Uuid": "{7bfb6e4a-6075-56da-8006-b262d99dff30}",
+        "InputStatsArrayPath": {
+            "Attribute Matrix Name": "CellEnsembleData",
+            "Data Array Name": "Statistics",
+            "Data Container Name": "StatsGeneratorDataContainer"
+        },
+        "MaxIterations": 100,
+        "NeighborListArrayPath": {
+            "Attribute Matrix Name": "Grain Data",
+            "Data Array Name": "NeighborList",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "NumFeaturesArrayPath": {
+            "Attribute Matrix Name": "CellEnsembleData",
+            "Data Array Name": "NumFeatures",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "PhaseTypesArrayPath": {
+            "Attribute Matrix Name": "CellEnsembleData",
+            "Data Array Name": "PhaseTypes",
+            "Data Container Name": "StatsGeneratorDataContainer"
+        },
+        "SharedSurfaceAreaListArrayPath": {
+            "Attribute Matrix Name": "Grain Data",
+            "Data Array Name": "SharedSurfaceAreaList",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "SurfaceFeaturesArrayPath": {
+            "Attribute Matrix Name": "Grain Data",
+            "Data Array Name": "SurfaceFeatures",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "VolumesArrayName": "Volumes"
+    },
+    "8": {
+        "CellEulerAnglesArrayPath": {
+            "Attribute Matrix Name": "CellData",
+            "Data Array Name": "EulerAngles",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "CellIPFColorsArrayName": "IPFColor",
+        "CellPhasesArrayPath": {
+            "Attribute Matrix Name": "CellData",
+            "Data Array Name": "Phases",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "CrystalStructuresArrayPath": {
+            "Attribute Matrix Name": "CellEnsembleData",
+            "Data Array Name": "CrystalStructures",
+            "Data Container Name": "StatsGeneratorDataContainer"
+        },
+        "FilterVersion": "6.5.138",
+        "Filter_Enabled": true,
+        "Filter_Human_Label": "Generate IPF Colors",
+        "Filter_Name": "GenerateIPFColors",
+        "Filter_Uuid": "{a50e6532-8075-5de5-ab63-945feb0de7f7}",
+        "GoodVoxelsArrayPath": {
+            "Attribute Matrix Name": "CellData",
+            "Data Array Name": "",
+            "Data Container Name": "SyntheticVolumeDataContainer"
+        },
+        "ReferenceDir": {
+            "x": 0,
+            "y": 0,
+            "z": 1
+        },
+        "UseGoodVoxels": 0
+    },
+    "9": {
+        "FilterVersion": "1.2.812",
+        "Filter_Enabled": true,
+        "Filter_Human_Label": "Write DREAM.3D Data File",
+        "Filter_Name": "DataContainerWriter",
+        "Filter_Uuid": "{3fcd4c43-9d75-5b86-aad4-4441bc914f37}",
+        "OutputFile": "C:\\Users\\work\\Desktop\\2phase_irregularGrid.dream3d",
+        "WriteTimeSeries": 0,
+        "WriteXdmfFile": 1
+    },
+    "PipelineBuilder": {
+        "Name": "2phase_irregularGrid",
+        "Number_Filters": 10,
+        "Version": 6
+    }
+}

python/tests/reference/Grid/2phase_irregularGrid.xdmf

@@ -0,0 +1,42 @@
+<?xml version="1.0"?>
+<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd"[]>
+<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
+ <Domain>
+  <!-- *************** START OF SyntheticVolumeDataContainer *************** -->
+  <Grid Name="SyntheticVolumeDataContainer" GridType="Uniform">
+    <Topology TopologyType="3DCoRectMesh" Dimensions="11 9 14 "></Topology>
+    <Geometry Type="ORIGIN_DXDYDZ">
+      <!-- Origin  Z, Y, X -->
+      <DataItem Format="XML" Dimensions="3">0 0 0</DataItem>
+      <!-- DxDyDz (Spacing/Resolution) Z, Y, X -->
+      <DataItem Format="XML" Dimensions="3">0.8 0.8 0.8</DataItem>
+    </Geometry>
+    <Attribute Name="BoundaryCells" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="10 8 13 1" NumberType="Char" Precision="1" >
+        2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/BoundaryCells
+      </DataItem>
+    </Attribute>
+    <Attribute Name="EulerAngles" AttributeType="Vector" Center="Cell">
+      <DataItem Format="HDF" Dimensions="10 8 13 3" NumberType="Float" Precision="4" >
+        2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/EulerAngles
+      </DataItem>
+    </Attribute>
+    <Attribute Name="FeatureIds" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="10 8 13 1" NumberType="Int" Precision="4" >
+        2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/FeatureIds
+      </DataItem>
+    </Attribute>
+    <Attribute Name="IPFColor" AttributeType="Vector" Center="Cell">
+      <DataItem Format="HDF" Dimensions="10 8 13 3" NumberType="UChar" Precision="1" >
+        2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/IPFColor
+      </DataItem>
+    </Attribute>
+    <Attribute Name="Phases" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="10 8 13 1" NumberType="Int" Precision="4" >
+        2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/Phases
+      </DataItem>
+    </Attribute>
+  </Grid>
+  <!-- *************** END OF SyntheticVolumeDataContainer *************** -->
+ </Domain>
+</Xdmf>

python/tests/reference/Grid/measured.xdmf

@@ -0,0 +1,77 @@
+<?xml version="1.0"?>
+<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd"[]>
+<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
+ <Domain>
+  <!-- *************** START OF Small IN100 *************** -->
+  <Grid Name="Small IN100" GridType="Uniform">
+    <Topology TopologyType="3DCoRectMesh" Dimensions="2 102 202 "></Topology>
+    <Geometry Type="ORIGIN_DXDYDZ">
+      <!-- Origin  Z, Y, X -->
+      <DataItem Format="XML" Dimensions="3">0 35 -294.7</DataItem>
+      <!-- DxDyDz (Spacing/Resolution) Z, Y, X -->
+      <DataItem Format="XML" Dimensions="3">0.35 0.35 0.35</DataItem>
+    </Geometry>
+    <Attribute Name="Confidence Index" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Confidence Index
+      </DataItem>
+    </Attribute>
+    <Attribute Name="EulerAngles" AttributeType="Vector" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 3" NumberType="Float" Precision="4" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/EulerAngles
+      </DataItem>
+    </Attribute>
+    <Attribute Name="FeatureIds" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Int" Precision="4" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/FeatureIds
+      </DataItem>
+    </Attribute>
+    <Attribute Name="Fit" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Fit
+      </DataItem>
+    </Attribute>
+    <Attribute Name="IPFColor" AttributeType="Vector" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 3" NumberType="UChar" Precision="1" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/IPFColor
+      </DataItem>
+    </Attribute>
+    <Attribute Name="Image Quality" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Image Quality
+      </DataItem>
+    </Attribute>
+    <Attribute Name="Mask" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="uchar" Precision="1" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Mask
+      </DataItem>
+    </Attribute>
+    <Attribute Name="ParentIds" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Int" Precision="4" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/ParentIds
+      </DataItem>
+    </Attribute>
+    <Attribute Name="Phases" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Int" Precision="4" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Phases
+      </DataItem>
+    </Attribute>
+    <Attribute Name="SEM Signal" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/SEM Signal
+      </DataItem>
+    </Attribute>
+    <Attribute Name="X Position" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/X Position
+      </DataItem>
+    </Attribute>
+    <Attribute Name="Y Position" AttributeType="Scalar" Center="Cell">
+      <DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
+        measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Y Position
+      </DataItem>
+    </Attribute>
+  </Grid>
+  <!-- *************** END OF Small IN100 *************** -->
+ </Domain>
+</Xdmf>

python/tests/reference/Result/12grains6x7x8_tensionY.yaml

@@ -2,15 +2,15 @@
 homogenization:
   SX:
     N_constituents: 1
-    mechanics: {type: none}
+    mechanical: {type: pass}
 
 phase:
   pheno_fcc:
     lattice: cF
-    mechanics:
+    mechanical:
       output: [F, P, F_e, F_p, L_p, O]
-      elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
+      elastic: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
-      plasticity:
+      plastic:
         N_sl: [12]
         a_sl: 2.25
         atol_xi: 1.0
@@ -24,10 +24,10 @@ phase:
         xi_inf_sl: [63e6]
   pheno_bcc:
     lattice: cI
-    mechanics:
+    mechanical:
       output: [F, P, F_e, F_p, L_p, O]
-      elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
+      elastic: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
-      plasticity:
+      plastic:
         N_sl: [12]
         a_sl: 2.25
         atol_xi: 1.0
@@ -42,62 +42,62 @@ phase:
 
 material:
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.8229200444892315, 0.5284940239127993, -0.11958598847729246, 0.17086795611292308]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.029934934533052786, -0.0463822071939717, 0.9983440440417412, 0.01617900728410769]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.5285808688806949, 0.7326575088838098, 0.4051997815944012, 0.1401013087924221]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.1839974517790312, 0.49550065903084944, -0.1541415483910751, -0.8347840545305227]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.8055693100147384, -0.22778497057116814, -0.028331746016454287, 0.5462320075864553]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.8025842700117737, -0.33640019337884963, -0.3847408071640489, 0.3076815085881779]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.6048933483394416, 0.7565005822419409, -0.08545681892422426, -0.2334695661144201]
         phase: pheno_bcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.2012339360745425, -0.3580127491130033, -0.7798091137625135, 0.47247171400774884]
         phase: pheno_bcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.7949688202267222, 0.3623793306926909, -0.18836147613310203, -0.4485819321629098]
         phase: pheno_bcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.19733162113429173, -0.06559103894055797, -0.40230149937129567, 0.8915781236183501]
         phase: pheno_bcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.8659916384140512, -0.2761459420825848, 0.38479354764225004, -0.1604238964779258]
         phase: pheno_bcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.5951846978175659, 0.4476701545571293, -0.6038886363266418, -0.2840160613735736]
         phase: pheno_bcc
     homogenization: SX

python/tests/reference/Result/6grains6x7x8_single_phase_tensionY.yaml

@@ -2,15 +2,15 @@
 homogenization:
   SX:
     N_constituents: 1
-    mechanics: {type: none}
+    mechanical: {type: pass}
 
 phase:
   pheno_fcc:
     lattice: cF
-    mechanics:
+    mechanical:
       output: [F, P, F_e, F_p, L_p, O]
-      elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
+      elastic: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
-      plasticity:
+      plastic:
         N_sl: [12]
         a_sl: 2.25
         atol_xi: 1.0
@@ -25,32 +25,32 @@ phase:
 
 material:
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.8229200444892315, 0.5284940239127993, -0.11958598847729246, 0.17086795611292308]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.029934934533052786, -0.0463822071939717, 0.9983440440417412, 0.01617900728410769]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.5285808688806949, 0.7326575088838098, 0.4051997815944012, 0.1401013087924221]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.1839974517790312, 0.49550065903084944, -0.1541415483910751, -0.8347840545305227]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.8055693100147384, -0.22778497057116814, -0.028331746016454287, 0.5462320075864553]
         phase: pheno_fcc
     homogenization: SX
   - constituents:
-      - fraction: 1.0
+      - v: 1.0
         O: [0.8025842700117737, -0.33640019337884963, -0.3847408071640489, 0.3076815085881779]
         phase: pheno_fcc
     homogenization: SX

python/tests/reference/Result/tensionY.yaml

@@ -1,14 +1,17 @@
 ---
+solver:
+  mechanical: spectral_basic
 
-step:
+loadstep:
-  - discretization:
+  - boundary_conditions:
-      t: 20
+      mechanical:
-      N: 40
-      f_out: 4
-    mechanics:
         dot_F: [x, 0,      0,
                 0, 1.0e-3, 0,
                 0, 0,      x]
         P: [0, x, x,
             x, x, x,
             x, x, 0]
+    discretization:
+      t: 20
+      N: 40
+    f_out: 4

python/tests/test_Config.py

@@ -2,6 +2,8 @@ import pytest
 import numpy as np
 
 from damask import Config
+from damask import Rotation
+from damask import Orientation
 
 class TestConfig:
 
@@ -51,3 +53,7 @@ class TestConfig:
 
     def test_abstract_is_complete(self):
         assert Config().is_complete is None
+    
+    @pytest.mark.parametrize('data',[Rotation.from_random(),Orientation.from_random()])
+    def test_rotation_orientation(self,data):
+        assert str(Config(a=data)) == str(Config(a=data.as_quaternion()))

python/tests/test_ConfigMaterial.py

@@ -1,11 +1,11 @@
 import os
-
 import pytest
 import numpy as np
 
 from damask import ConfigMaterial
 from damask import Table
 from damask import Rotation
+from damask import Grid
 
 @pytest.fixture
 def ref_path(ref_path_base):
@@ -108,3 +108,35 @@ class TestConfigMaterial:
         m = ConfigMaterial().material_add(**kw)
         assert len(m['material']) == N
         assert len(m['material'][0]['constituents']) == n
+
+
+    @pytest.mark.parametrize('cell_ensemble_data',[None,'CellEnsembleData'])
+    def test_load_DREAM3D(self,ref_path,cell_ensemble_data):
+        grain_c = ConfigMaterial.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','Grain Data',
+                  cell_ensemble_data = cell_ensemble_data)
+        point_c = ConfigMaterial.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d',
+                  cell_ensemble_data = cell_ensemble_data)
+
+        assert point_c.is_valid and grain_c.is_valid and \
+               len(point_c['material'])+1 == len(grain_c['material'])
+
+        grain_m = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','FeatureIds').material.flatten()
+        point_m = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d').material.flatten()
+
+        for i in np.unique(point_m):
+            j = int(grain_m[(point_m==i).nonzero()[0][0]])
+            assert np.allclose(point_c['material'][i]['constituents'][0]['O'],
+                               grain_c['material'][j]['constituents'][0]['O'])
+            assert point_c['material'][i]['constituents'][0]['phase'] == \
+                   grain_c['material'][j]['constituents'][0]['phase']
+
+
+    def test_load_DREAM3D_reference(self,tmp_path,ref_path,update):
+        cur = ConfigMaterial.load_DREAM3D(ref_path/'measured.dream3d')
+        ref = ConfigMaterial.load(ref_path/'measured.material_yaml')
+        if update:
+            cur.save(ref_path/'measured.material_yaml')
+        for i,m in enumerate(ref['material']):
+            assert Rotation(m['constituents'][0]['O']) == \
+                   Rotation(cur['material'][i]['constituents'][0]['O'])
+        assert cur.is_valid and cur['phase'] == ref['phase'] and cur['homogenization'] == ref['homogenization']

python/tests/test_Grid.py

@@ -420,12 +420,31 @@ class TestGrid:
         t = Table(np.column_stack((coords.reshape(-1,3,order='F'),grid.material.flatten(order='F'))),{'c':3,'m':1})
         assert grid_equal(grid.sort().renumber(),Grid.from_table(t,'c',['m']))
 
+
     @pytest.mark.parametrize('periodic',[True,False])
     @pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
     def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
-        grid=Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
+        grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
-        current=grid.get_grain_boundaries(periodic,direction)
+        current = grid.get_grain_boundaries(periodic,direction)
         if update:
             current.save(ref_path/f'get_grain_boundaries_8g12x15x20_{direction}_{periodic}.vtu',parallel=False)
-        reference=VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
+        reference = VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
         assert current.__repr__() == reference.__repr__()
+
+
+    def test_load_DREAM3D(self,ref_path):
+        grain = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','FeatureIds')
+        point = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d')
+
+        assert np.allclose(grain.origin,point.origin) and \
+               np.allclose(grain.size,point.size) and \
+               (grain.sort().material == point.material+1).all()
+
+
+    def test_load_DREAM3D_reference(self,ref_path,update):
+        current   = Grid.load_DREAM3D(ref_path/'measured.dream3d')
+        reference = Grid.load(ref_path/'measured')
+        if update:
+            current.save(ref_path/'measured.vtr')
+
+        assert grid_equal(current,reference)

python/tests/test_Result.py

@@ -48,7 +48,7 @@ class TestResult:
         a = default.get_dataset_location('F')
         default.view('increments','*')
         b = default.get_dataset_location('F')
-        default.view('increments',default.incs_in_range(0,np.iinfo(int).max))
+        default.view('increments',default.increments_in_range(0,np.iinfo(int).max))
         c = default.get_dataset_location('F')
 
         default.view('times',True)
@@ -173,7 +173,7 @@ class TestResult:
         loc = {'O':     default.get_dataset_location('O'),
                'color': default.get_dataset_location('IPFcolor_[{} {} {}]'.format(*d))}
         qu = default.read_dataset(loc['O']).view(np.double).squeeze()
-        crystal_structure = default._get_attribute(default.get_dataset_location('O')[0],'Lattice')
+        crystal_structure = default._get_attribute(default.get_dataset_location('O')[0],'lattice')
         c = Orientation(rotation=qu,lattice=crystal_structure)
         in_memory = np.uint8(c.IPF_color(np.array(d))*255)
         in_file = default.read_dataset(loc['color'])
@@ -314,9 +314,9 @@ class TestResult:
         with h5py.File(default.fname,'r') as f:
             # h5py3 compatibility
             try:
-                created_first = f[loc[0]].attrs['Created'].decode()
+                created_first = f[loc[0]].attrs['created'].decode()
             except AttributeError:
-                created_first = f[loc[0]].attrs['Created']
+                created_first = f[loc[0]].attrs['created']
         created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
 
         if overwrite == 'on':
@@ -332,9 +332,9 @@ class TestResult:
         with h5py.File(default.fname,'r') as f:
             # h5py3 compatibility
             try:
-                created_second = f[loc[0]].attrs['Created'].decode()
+                created_second = f[loc[0]].attrs['created'].decode()
             except AttributeError:
-                created_second = f[loc[0]].attrs['Created']
+                created_second = f[loc[0]].attrs['created']
         created_second = datetime.strptime(created_second,'%Y-%m-%d %H:%M:%S%z')
         if overwrite == 'on':
             assert created_first < created_second and np.allclose(default.read_dataset(loc),311.)

python/tests/test_util.py

@@ -1,6 +1,10 @@
+import random
+import os
+
 import pytest
 import numpy as np
 from scipy import stats
+import h5py
 
 from damask import util
 
@@ -102,3 +106,36 @@ class TestUtil:
     @pytest.mark.parametrize('style',[util.emph,util.deemph,util.warn,util.strikeout])
     def test_decorate(self,style):
         assert 'DAMASK' in style('DAMASK')
+
+    @pytest.mark.parametrize('complete',[True,False])
+    def test_D3D_base_group(self,tmp_path,complete):
+        base_group = ''.join(random.choices('DAMASK', k=10))
+        with h5py.File(tmp_path/'base_group.dream3d','w') as f:
+            f.create_group(os.path.join(base_group,'_SIMPL_GEOMETRY'))
+            if complete:
+                f[os.path.join(base_group,'_SIMPL_GEOMETRY')].create_dataset('SPACING',data=np.ones(3))
+
+        if complete:
+            assert base_group == util.DREAM3D_base_group(tmp_path/'base_group.dream3d')
+        else:
+            with pytest.raises(ValueError):
+                util.DREAM3D_base_group(tmp_path/'base_group.dream3d')
+
+    @pytest.mark.parametrize('complete',[True,False])
+    def test_D3D_cell_data_group(self,tmp_path,complete):
+        base_group = ''.join(random.choices('DAMASK', k=10))
+        cell_data_group = ''.join(random.choices('KULeuven', k=10))
+        cells = np.random.randint(1,50,3)
+        with h5py.File(tmp_path/'cell_data_group.dream3d','w') as f:
+            f.create_group(os.path.join(base_group,'_SIMPL_GEOMETRY'))
+            f[os.path.join(base_group,'_SIMPL_GEOMETRY')].create_dataset('SPACING',data=np.ones(3))
+            f[os.path.join(base_group,'_SIMPL_GEOMETRY')].create_dataset('DIMENSIONS',data=cells[::-1])
+            f[base_group].create_group(cell_data_group)
+            if complete:
+                f[os.path.join(base_group,cell_data_group)].create_dataset('data',shape=np.append(cells,1))
+
+        if complete:
+            assert cell_data_group == util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')
+        else:
+            with pytest.raises(ValueError):
+                util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')

src/DAMASK_interface.f90

@@ -93,7 +93,7 @@ subroutine DAMASK_interface_init
 #endif
   print*, achar(27)//'[0m'
 
-  print*, 'Roters et al., Computational Materials Science 158:420–478, 2019'
+  print*, 'F. Roters et al., Computational Materials Science 158:420–478, 2019'
   print*, 'https://doi.org/10.1016/j.commatsci.2018.04.030'
 
   print'(/,a)', ' Version: '//DAMASKVERSION

src/grid/DAMASK_grid.f90

@@ -104,7 +104,6 @@ program DAMASK_grid
     load_step, &
     solver, &
     initial_conditions, &
-    ic_thermal, &
     thermal, &
     step_bc, &
     step_mech, &
@@ -118,7 +117,7 @@ program DAMASK_grid
   call CPFEM_initAll
   print'(/,a)',   ' <<<+-  DAMASK_grid init  -+>>>'; flush(IO_STDOUT)
 
-  print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
+  print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
   print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
 
 

src/grid/grid_damage_spectral.f90

@@ -75,7 +75,7 @@ subroutine grid_damage_spectral_init
 
   print'(/,a)', ' <<<+-  grid_spectral_damage init  -+>>>'
 
-  print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
+  print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
   print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
 
 !-------------------------------------------------------------------------------------------------

src/grid/grid_mech_spectral_basic.f90

@@ -105,10 +105,10 @@ subroutine grid_mechanical_spectral_basic_init
 
   print'(/,a)', ' <<<+-  grid_mechanical_spectral_basic init  -+>>>'; flush(IO_STDOUT)
 
-  print*, 'Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
+  print*, 'P. Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
   print*, 'https://doi.org/10.1016/j.ijplas.2012.09.012'//IO_EOL
 
-  print*, 'Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
+  print*, 'P. Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
   print*, 'https://doi.org/10.1016/j.ijplas.2014.02.006'
 
 !-------------------------------------------------------------------------------------------------

src/grid/grid_mech_spectral_polarisation.f90

@@ -118,7 +118,7 @@ subroutine grid_mechanical_spectral_polarisation_init
 
   print'(/,a)', ' <<<+-  grid_mechanical_spectral_polarization init  -+>>>'; flush(IO_STDOUT)
 
-  print*, 'Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
+  print*, 'P. Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
   print*, 'https://doi.org/10.1016/j.ijplas.2014.02.006'
 
 !-------------------------------------------------------------------------------------------------

src/grid/grid_thermal_spectral.f90

@@ -75,7 +75,7 @@ subroutine grid_thermal_spectral_init(T_0)
 
   print'(/,a)', ' <<<+-  grid_thermal_spectral init  -+>>>'
 
-  print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
+  print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
   print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
 
 !-------------------------------------------------------------------------------------------------

src/grid/spectral_utilities.f90

@@ -176,16 +176,16 @@ subroutine spectral_utilities_init
 
   print'(/,a)', ' <<<+-  spectral_utilities init  -+>>>'
 
-  print*, 'Diehl, Diploma Thesis TU München, 2010'
+  print*, 'M. Diehl, Diploma Thesis TU München, 2010'
   print*, 'https://doi.org/10.13140/2.1.3234.3840'//IO_EOL
 
-  print*, 'Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
+  print*, 'P. Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
   print*, 'https://doi.org/10.1016/j.ijplas.2012.09.012'//IO_EOL
 
-  print*, 'Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
+  print*, 'P. Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
   print*, 'https://doi.org/10.1016/j.ijplas.2014.02.006'//IO_EOL
 
-  print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
+  print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
   print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
 
 !--------------------------------------------------------------------------------------------------

src/homogenization.f90

@@ -276,8 +276,8 @@ subroutine materialpoint_stressAndItsTangent(dt,FEsolving_execIP,FEsolving_execE
 
       call phase_restore(ce,.false.) ! wrong name (is more a forward function)
 
-      if(homogState(ho)%sizeState > 0)  homogState(ho)%State(:,me) = homogState(ho)%State0(:,me)
+      if(homogState(ho)%sizeState > 0)  homogState(ho)%state(:,me) = homogState(ho)%state0(:,me)
-      if(damageState_h(ho)%sizeState > 0) damageState_h(ho)%State(:,me) = damageState_h(ho)%State0(:,me)
+      if(damageState_h(ho)%sizeState > 0) damageState_h(ho)%state(:,me) = damageState_h(ho)%state0(:,me)
       call damage_partition(ce)
 
       doneAndHappy = [.false.,.true.]
@@ -287,20 +287,17 @@ subroutine materialpoint_stressAndItsTangent(dt,FEsolving_execIP,FEsolving_execE
                                     .and. NiterationMPstate < num%nMPstate)
         NiterationMPstate = NiterationMPstate + 1
 
-
-        if (.not. doneAndHappy(1)) then
         call mechanical_partition(homogenization_F(1:3,1:3,ce),ce)
         converged = .true.
         do co = 1, myNgrains
           converged = converged .and. crystallite_stress(dt,co,ip,el)
         enddo
 
-          if (.not. converged) then
+        if (converged) then
-            doneAndHappy = [.true.,.false.]
-          else
           doneAndHappy = mechanical_updateState(dt,homogenization_F(1:3,1:3,ce),ce)
           converged = all(doneAndHappy)
-          endif
+        else
+          doneAndHappy = [.true.,.false.]
         endif
 
       enddo convergenceLooping
@@ -370,17 +367,17 @@ subroutine homogenization_results
 
     call mechanical_results(group_base,ho)
 
-    group = trim(group_base)//'/damage'
-    call results_closeGroup(results_addGroup(group))
     select case(damage_type(ho))
       case(DAMAGE_NONLOCAL_ID)
+        group = trim(group_base)//'/damage'
+        call results_closeGroup(results_addGroup(group))
         call damage_nonlocal_results(ho,group)
     end select
 
-    group = trim(group_base)//'/thermal'
-    call results_closeGroup(results_addGroup(group))
     select case(thermal_type(ho))
       case(THERMAL_CONDUCTION_ID)
+        group = trim(group_base)//'/thermal'
+        call results_closeGroup(results_addGroup(group))
         call thermal_conduction_results(ho,group)
     end select
 
@@ -450,7 +447,7 @@ subroutine homogenization_restartRead(fileHandle)
 
     groupHandle(2) = HDF5_openGroup(groupHandle(1),material_name_homogenization(ho))
 
-    call HDF5_read(groupHandle(2),homogState(ho)%state,'omega') ! ToDo: should be done by mech
+    call HDF5_read(groupHandle(2),homogState(ho)%state0,'omega') ! ToDo: should be done by mech
 
     call HDF5_closeGroup(groupHandle(2))
 
@@ -545,7 +542,7 @@ subroutine material_parseHomogenization
 
   do h=1, size(material_name_homogenization)
     homog => material_homogenization%get(h)
-    homogMech => homog%get('mechanics')
+    homogMech => homog%get('mechanical')
     select case (homogMech%get_asString('type'))
       case('pass')
         homogenization_type(h) = HOMOGENIZATION_NONE_ID

src/homogenization_mechanical.f90

@@ -224,7 +224,7 @@ module subroutine mechanical_results(group_base,ho)
 
   character(len=:), allocatable :: group
 
-  group = trim(group_base)//'/mech'
+  group = trim(group_base)//'/mechanical'
   call results_closeGroup(results_addGroup(group))
 
   select case(homogenization_type(ho))

src/homogenization_mechanical_RGC.f90

@@ -91,14 +91,13 @@ module subroutine mechanical_RGC_init(num_homogMech)
 
   print'(a,i2)', ' # instances: ',count(homogenization_type == HOMOGENIZATION_RGC_ID); flush(IO_STDOUT)
 
-  print*, 'Tjahjanto et al., International Journal of Material Forming 2(1):939–942, 2009'
+  print*, 'D.D. Tjahjanto et al., International Journal of Material Forming 2(1):939–942, 2009'
   print*, 'https://doi.org/10.1007/s12289-009-0619-1'//IO_EOL
 
-  print*, 'Tjahjanto et al., Modelling and Simulation in Materials Science and Engineering 18:015006, 2010'
+  print*, 'D.D. Tjahjanto et al., Modelling and Simulation in Materials Science and Engineering 18:015006, 2010'
   print*, 'https://doi.org/10.1088/0965-0393/18/1/015006'//IO_EOL
 
 
-
   material_homogenization => config_material%get('homogenization')
   allocate(param(material_homogenization%length))
   allocate(state(material_homogenization%length))
@@ -139,7 +138,7 @@ module subroutine mechanical_RGC_init(num_homogMech)
   do ho = 1, size(homogenization_type)
     if (homogenization_type(ho) /= HOMOGENIZATION_RGC_ID) cycle
     homog => material_homogenization%get(ho)
-    homogMech => homog%get('mechanics')
+    homogMech => homog%get('mechanical')
     associate(prm => param(ho), &
               stt => state(ho), &
               st0 => state0(ho), &

src/homogenization_mechanical_isostrain.f90

@@ -46,7 +46,7 @@ module subroutine mechanical_isostrain_init
   do h = 1, size(homogenization_type)
     if (homogenization_type(h) /= HOMOGENIZATION_ISOSTRAIN_ID) cycle
     homog => material_homogenization%get(h)
-    homogMech => homog%get('mechanics')
+    homogMech => homog%get('mechanical')
     associate(prm => param(h))
 
     prm%N_constituents = homogenization_Nconstituents(h)

src/lattice.f90

@@ -480,8 +480,8 @@ subroutine lattice_init
 
   do ph = 1, phases%length
     phase => phases%get(ph)
-    mech  => phase%get('mechanics')
+    mech  => phase%get('mechanical')
-    elasticity => mech%get('elasticity')
+    elasticity => mech%get('elastic')
     lattice_C66(1,1,ph) = elasticity%get_asFloat('C_11')
     lattice_C66(1,2,ph) = elasticity%get_asFloat('C_12')
 

src/phase_damage.f90

@@ -341,21 +341,21 @@ module subroutine damage_results(group,ph)
   sourceLoop: do so = 1, phase_Nsources(ph)
 
   if (phase_source(ph) /= DAMAGE_UNDEFINED_ID) &
-    call results_closeGroup(results_addGroup(group//'sources/')) ! should be 'damage'
+    call results_closeGroup(results_addGroup(group//'damage'))
 
     sourceType: select case (phase_source(ph))
 
       case (DAMAGE_ISOBRITTLE_ID) sourceType
-        call isobrittle_results(ph,group//'sources/')
+        call isobrittle_results(ph,group//'damage/')
 
       case (DAMAGE_ISODUCTILE_ID) sourceType
-        call isoductile_results(ph,group//'sources/')
+        call isoductile_results(ph,group//'damage/')
 
       case (DAMAGE_ANISOBRITTLE_ID) sourceType
-        call anisobrittle_results(ph,group//'sources/')
+        call anisobrittle_results(ph,group//'damage/')
 
       case (DAMAGE_ANISODUCTILE_ID) sourceType
-        call anisoductile_results(ph,group//'sources/')
+        call anisoductile_results(ph,group//'damage/')
 
     end select sourceType
 

src/phase_damage_anisoductile.f90

@@ -53,8 +53,8 @@ module function anisoductile_init() result(mySources)
   do p = 1, phases%length
     if(mySources(p)) then
       phase => phases%get(p)
-      mech  => phase%get('mechanics')
+      mech  => phase%get('mechanical')
-      pl    => mech%get('plasticity')
+      pl    => mech%get('plastic')
       sources => phase%get('damage')
 
 

src/phase_mechanical.f90

@@ -247,13 +247,13 @@ module subroutine mechanical_init(materials,phases)
     allocate(phase_mechanical_F0(ph)%data(3,3,Nmembers))
 
     phase   => phases%get(ph)
-    mech    => phase%get('mechanics')
+    mech    => phase%get('mechanical')
 #if defined(__GFORTRAN__)
     output_constituent(ph)%label  = output_as1dString(mech)
 #else
     output_constituent(ph)%label  = mech%get_as1dString('output',defaultVal=emptyStringArray)
 #endif
-    elastic => mech%get('elasticity')
+    elastic => mech%get('elastic')
     if(elastic%get_asString('type') == 'hooke') then
       phase_elasticity(ph) = ELASTICITY_HOOKE_ID
     else
@@ -269,7 +269,7 @@ module subroutine mechanical_init(materials,phases)
   if(maxVal(phase_NstiffnessDegradations)/=0) then
     do ph = 1, phases%length
       phase => phases%get(ph)
-      mech    => phase%get('mechanics')
+      mech    => phase%get('mechanical')
       stiffDegradation => mech%get('stiffness_degradation',defaultVal=emptyList)
       do stiffDegradationCtr = 1, stiffDegradation%length
         if(stiffDegradation%get_asString(stiffDegradationCtr) == 'damage') &
@@ -398,32 +398,31 @@ module subroutine mechanical_results(group,ph)
   character(len=*), intent(in) :: group
   integer,          intent(in) :: ph
 
-  if (phase_plasticity(ph) /= PLASTICITY_NONE_ID) &
+
-    call results_closeGroup(results_addGroup(group//'plastic/'))
+  call crystallite_results(group,ph)
 
   select case(phase_plasticity(ph))
 
     case(PLASTICITY_ISOTROPIC_ID)
-      call plastic_isotropic_results(ph,group//'plastic/')
+      call plastic_isotropic_results(ph,group//'mechanical/')
 
     case(PLASTICITY_PHENOPOWERLAW_ID)
-      call plastic_phenopowerlaw_results(ph,group//'plastic/')
+      call plastic_phenopowerlaw_results(ph,group//'mechanical/')
 
     case(PLASTICITY_KINEHARDENING_ID)
-      call plastic_kinehardening_results(ph,group//'plastic/')
+      call plastic_kinehardening_results(ph,group//'mechanical/')
 
     case(PLASTICITY_DISLOTWIN_ID)
-      call plastic_dislotwin_results(ph,group//'plastic/')
+      call plastic_dislotwin_results(ph,group//'mechanical/')
 
     case(PLASTICITY_DISLOTUNGSTEN_ID)
-      call plastic_dislotungsten_results(ph,group//'plastic/')
+      call plastic_dislotungsten_results(ph,group//'mechanical/')
 
     case(PLASTICITY_NONLOCAL_ID)
-      call plastic_nonlocal_results(ph,group//'plastic/')
+      call plastic_nonlocal_results(ph,group//'mechanical/')
 
   end select
 
-  call crystallite_results(group,ph)
 
 end subroutine mechanical_results
 
@@ -561,7 +560,7 @@ function integrateStress(F,subFp0,subFi0,Delta_t,co,ip,el) result(broken)
         cycle LpLoop
       endif
 
-      calculateJacobiLi: if (mod(jacoCounterLp, num%iJacoLpresiduum) == 0) then
+      calculateJacobiLp: if (mod(jacoCounterLp, num%iJacoLpresiduum) == 0) then
         jacoCounterLp = jacoCounterLp + 1
 
         do o=1,3; do p=1,3
@@ -573,7 +572,7 @@ function integrateStress(F,subFp0,subFi0,Delta_t,co,ip,el) result(broken)
         call dgesv(9,1,dRLp_dLp,9,devNull_9,temp_9,9,ierr)                                          ! solve dRLp/dLp * delta Lp = -res for delta Lp
         if (ierr /= 0) return ! error
         deltaLp = - math_9to33(temp_9)
-      endif calculateJacobiLi
+      endif calculateJacobiLp
 
       Lpguess = Lpguess &
               + deltaLp * steplengthLp
@@ -601,7 +600,7 @@ function integrateStress(F,subFp0,subFi0,Delta_t,co,ip,el) result(broken)
       cycle LiLoop
     endif
 
-    calculateJacobiLp: if (mod(jacoCounterLi, num%iJacoLpresiduum) == 0) then
+    calculateJacobiLi: if (mod(jacoCounterLi, num%iJacoLpresiduum) == 0) then
       jacoCounterLi = jacoCounterLi + 1
 
       temp_33 = matmul(matmul(A,B),invFi_current)
@@ -620,7 +619,7 @@ function integrateStress(F,subFp0,subFi0,Delta_t,co,ip,el) result(broken)
       call dgesv(9,1,dRLi_dLi,9,devNull_9,temp_9,9,ierr)                                            ! solve dRLi/dLp * delta Li = -res for delta Li
       if (ierr /= 0) return ! error
       deltaLi = - math_9to33(temp_9)
-    endif calculateJacobiLp
+    endif calculateJacobiLi
 
     Liguess = Liguess &
             + deltaLi * steplengthLi
@@ -978,35 +977,35 @@ subroutine crystallite_results(group,ph)
   character(len=:), allocatable              :: structureLabel
 
 
-    call results_closeGroup(results_addGroup(group//'/mechanics/'))
+    call results_closeGroup(results_addGroup(group//'/mechanical'))
 
     do ou = 1, size(output_constituent(ph)%label)
 
       select case (output_constituent(ph)%label(ou))
         case('F')
-          call results_writeDataset(group//'/mechanics/',phase_mechanical_F(ph)%data,'F',&
+          call results_writeDataset(group//'/mechanical/',phase_mechanical_F(ph)%data,'F',&
                                    'deformation gradient','1')
         case('F_e')
-          call results_writeDataset(group//'/mechanics/',phase_mechanical_Fe(ph)%data,'F_e',&
+          call results_writeDataset(group//'/mechanical/',phase_mechanical_Fe(ph)%data,'F_e',&
                                    'elastic deformation gradient','1')
         case('F_p')
-          call results_writeDataset(group//'/mechanics/',phase_mechanical_Fp(ph)%data,'F_p', &
+          call results_writeDataset(group//'/mechanical/',phase_mechanical_Fp(ph)%data,'F_p', &
                                    'plastic deformation gradient','1')
         case('F_i')
-          call results_writeDataset(group//'/mechanics/',phase_mechanical_Fi(ph)%data,'F_i', &
+          call results_writeDataset(group//'/mechanical/',phase_mechanical_Fi(ph)%data,'F_i', &
                                    'inelastic deformation gradient','1')
         case('L_p')
-          call results_writeDataset(group//'/mechanics/',phase_mechanical_Lp(ph)%data,'L_p', &
+          call results_writeDataset(group//'/mechanical/',phase_mechanical_Lp(ph)%data,'L_p', &
                                    'plastic velocity gradient','1/s')
         case('L_i')
-          call results_writeDataset(group//'/mechanics/',phase_mechanical_Li(ph)%data,'L_i', &
+          call results_writeDataset(group//'/mechanical/',phase_mechanical_Li(ph)%data,'L_i', &
                                    'inelastic velocity gradient','1/s')
         case('P')
-          call results_writeDataset(group//'/mechanics/',phase_mechanical_P(ph)%data,'P', &
+          call results_writeDataset(group//'/mechanical/',phase_mechanical_P(ph)%data,'P', &
-                                   'First Piola-Kirchhoff stress','Pa')
+                                   'first Piola-Kirchhoff stress','Pa')
         case('S')
-          call results_writeDataset(group//'/mechanics/',phase_mechanical_S(ph)%data,'S', &
+          call results_writeDataset(group//'/mechanical/',phase_mechanical_S(ph)%data,'S', &
-                                   'Second Piola-Kirchhoff stress','Pa')
+                                   'second Piola-Kirchhoff stress','Pa')
         case('O')
           select case(lattice_structure(ph))
             case(lattice_ISO_ID)
@@ -1023,9 +1022,9 @@ subroutine crystallite_results(group,ph)
               structureLabel = 'oP'
           end select
           selected_rotations = select_rotations(crystallite_orientation,ph)
-          call results_writeDataset(group//'/mechanics/',selected_rotations,output_constituent(ph)%label(ou),&
+          call results_writeDataset(group//'/mechanical',selected_rotations,output_constituent(ph)%label(ou),&
                                    'crystal orientation as quaternion','q_0 (q_1 q_2 q_3)')
-          call results_addAttribute('Lattice',structureLabel,group//'/mechanics/'//output_constituent(ph)%label(ou))
+          call results_addAttribute('lattice',structureLabel,group//'/mechanical/'//output_constituent(ph)%label(ou))
       end select
     enddo
 

src/phase_mechanical_eigen.f90

@@ -57,7 +57,7 @@ module subroutine eigendeformation_init(phases)
 
   do ph = 1,phases%length
     phase => phases%get(ph)
-    mechanics => phase%get('mechanics')
+    mechanics => phase%get('mechanical')
     kinematics => mechanics%get('eigen',defaultVal=emptyList)
     Nmodels(ph) = kinematics%length
   enddo
@@ -98,7 +98,7 @@ function kinematics_active(kinematics_label,kinematics_length)  result(active_ki
   allocate(active_kinematics(kinematics_length,phases%length), source = .false. )
   do p = 1, phases%length
     phase => phases%get(p)
-    mechanics => phase%get('mechanics')
+    mechanics => phase%get('mechanical')
     kinematics => mechanics%get('eigen',defaultVal=emptyList)
     do k = 1, kinematics%length
       kinematics_type => kinematics%get(k)

src/phase_mechanical_eigen_cleavageopening.f90

@@ -27,6 +27,4 @@ module function kinematics_cleavage_opening_init() result(myKinematics)
 end function kinematics_cleavage_opening_init
 
 
-
-
 end submodule cleavageopening

src/phase_mechanical_eigen_slipplaneopening.f90

@@ -61,8 +61,8 @@ module function kinematics_slipplane_opening_init() result(myKinematics)
   do p = 1, phases%length
     if(myKinematics(p)) then
       phase => phases%get(p)
-      mech  => phase%get('mechanics')
+      mech  => phase%get('mechanical')
-      pl    => mech%get('plasticity')
+      pl    => mech%get('plastic')
 
       kinematics => phase%get('damage')
 

src/phase_mechanical_plastic.f90

@@ -449,8 +449,8 @@ function plastic_active(plastic_label)  result(active_plastic)
   allocate(active_plastic(phases%length), source = .false. )
   do ph = 1, phases%length
     phase => phases%get(ph)
-    mech  => phase%get('mechanics')
+    mech  => phase%get('mechanical')
-    pl    => mech%get('plasticity')
+    pl    => mech%get('plastic')
     if(pl%get_asString('type') == plastic_label) active_plastic(ph) = .true.
   enddo
 

src/phase_mechanical_plastic_dislotungsten.f90

@@ -103,8 +103,8 @@ module function plastic_dislotungsten_init() result(myPlasticity)
   print'(/,a)', ' <<<+-  phase:mechanical:plastic:dislotungsten init  -+>>>'
   print'(a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
 
-  print*, 'Cereceda et al., International Journal of Plasticity 78:242–256, 2016'
+  print*, 'D. Cereceda et al., International Journal of Plasticity 78:242–256, 2016'
-  print*, 'https://dx.doi.org/10.1016/j.ijplas.2015.09.002'
+  print*, 'https://doi.org/10.1016/j.ijplas.2015.09.002'
 
 
   phases => config_material%get('phase')
@@ -120,8 +120,8 @@ module function plastic_dislotungsten_init() result(myPlasticity)
     associate(prm => param(ph), dot => dotState(ph), stt => state(ph), dst => dependentState(ph))
 
     phase => phases%get(ph)
-    mech  => phase%get('mechanics')
+    mech  => phase%get('mechanical')
-    pl  => mech%get('plasticity')
+    pl  => mech%get('plastic')
 
 #if defined (__GFORTRAN__)
     prm%output = output_as1dString(pl)

src/phase_mechanical_plastic_dislotwin.f90

@@ -150,13 +150,13 @@ module function plastic_dislotwin_init() result(myPlasticity)
   print'(/,a)', ' <<<+-  phase:mechanical:plastic:dislotwin init  -+>>>'
   print'(a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
 
-  print*, 'Ma and Roters, Acta Materialia 52(12):3603–3612, 2004'
+  print*, 'A. Ma and F. Roters, Acta Materialia 52(12):3603–3612, 2004'
   print*, 'https://doi.org/10.1016/j.actamat.2004.04.012'//IO_EOL
 
-  print*, 'Roters et al., Computational Materials Science 39:91–95, 2007'
+  print*, 'F. Roters et al., Computational Materials Science 39:91–95, 2007'
   print*, 'https://doi.org/10.1016/j.commatsci.2006.04.014'//IO_EOL
 
-  print*, 'Wong et al., Acta Materialia 118:140–151, 2016'
+  print*, 'S.L. Wong et al., Acta Materialia 118:140–151, 2016'
   print*, 'https://doi.org/10.1016/j.actamat.2016.07.032'
 
 
@@ -173,8 +173,8 @@ module function plastic_dislotwin_init() result(myPlasticity)
     associate(prm => param(ph), dot => dotState(ph), stt => state(ph), dst => dependentState(ph))
 
     phase => phases%get(ph)
-    mech  => phase%get('mechanics')
+    mech  => phase%get('mechanical')
-    pl  => mech%get('plasticity')
+    pl  => mech%get('plastic')
 
 #if defined (__GFORTRAN__)
     prm%output = output_as1dString(pl)

src/phase_mechanical_plastic_isotropic.f90

@@ -71,7 +71,7 @@ module function plastic_isotropic_init() result(myPlasticity)
   print'(/,a)', ' <<<+-  phase:mechanical:plastic:isotropic init  -+>>>'
   print'(a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
 
-  print*, 'Maiti and Eisenlohr, Scripta Materialia 145:37–40, 2018'
+  print*, 'T. Maiti and P. Eisenlohr, Scripta Materialia 145:37–40, 2018'
   print*, 'https://doi.org/10.1016/j.scriptamat.2017.09.047'
 
   phases => config_material%get('phase')
@@ -85,8 +85,8 @@ module function plastic_isotropic_init() result(myPlasticity)
     associate(prm => param(ph), dot => dotState(ph), stt => state(ph))
 
     phase => phases%get(ph)
-    mech  => phase%get('mechanics')
+    mech  => phase%get('mechanical')
-    pl  => mech%get('plasticity')
+    pl  => mech%get('plastic')
 
 #if defined (__GFORTRAN__)
     prm%output = output_as1dString(pl)

src/phase_mechanical_plastic_kinehardening.f90

@@ -98,8 +98,8 @@ module function plastic_kinehardening_init() result(myPlasticity)
     associate(prm => param(ph), dot => dotState(ph), dlt => deltaState(ph), stt => state(ph))
 
     phase => phases%get(ph)
-    mech  => phase%get('mechanics')
+    mech  => phase%get('mechanical')
-    pl  => mech%get('plasticity')
+    pl  => mech%get('plastic')
 
 #if defined (__GFORTRAN__)
     prm%output = output_as1dString(pl)

src/phase_mechanical_plastic_nonlocal.f90

@@ -203,10 +203,10 @@ module function plastic_nonlocal_init() result(myPlasticity)
   print'(/,a)', ' <<<+-  phase:mechanical:plastic:nonlocal init  -+>>>'
   print'(a,i0)', ' # phases: ',Ninstances; flush(IO_STDOUT)
 
-  print*, 'Reuber et al., Acta Materialia 71:333–348, 2014'
+  print*, 'C. Reuber et al., Acta Materialia 71:333–348, 2014'
   print*, 'https://doi.org/10.1016/j.actamat.2014.03.012'//IO_EOL
 
-  print*, 'Kords, Dissertation RWTH Aachen, 2014'
+  print*, 'C. Kords, Dissertation RWTH Aachen, 2014'
   print*, 'http://publications.rwth-aachen.de/record/229993'
 
 
@@ -227,8 +227,8 @@ module function plastic_nonlocal_init() result(myPlasticity)
               st0 => state0(ph), del => deltaState(ph), dst => microstructure(ph))
 
     phase => phases%get(ph)
-    mech  => phase%get('mechanics')
+    mech  => phase%get('mechanical')
-    pl  => mech%get('plasticity')
+    pl  => mech%get('plastic')
 
     phase_localPlasticity(ph) = .not. pl%contains('nonlocal')
 

src/phase_mechanical_plastic_phenopowerlaw.f90

@@ -107,8 +107,8 @@ module function plastic_phenopowerlaw_init() result(myPlasticity)
     associate(prm => param(ph), dot => dotState(ph), stt => state(ph))
 
     phase => phases%get(ph)
-    mech  => phase%get('mechanics')
+    mech  => phase%get('mechanical')
-    pl  => mech%get('plasticity')
+    pl  => mech%get('plastic')
 
 !--------------------------------------------------------------------------------------------------
 ! slip related parameters

src/results.f90

@@ -61,17 +61,18 @@ subroutine results_init(restart)
 
   print'(/,a)', ' <<<+-  results init  -+>>>'; flush(IO_STDOUT)
 
-  print*, 'Diehl et al., Integrating Materials and Manufacturing Innovation 6(1):83–91, 2017'
+  print*, 'M. Diehl et al., Integrating Materials and Manufacturing Innovation 6(1):83–91, 2017'
   print*, 'https://doi.org/10.1007/s40192-017-0084-5'//IO_EOL
 
   if(.not. restart) then
     resultsFile = HDF5_openFile(getSolverJobName()//'.hdf5','w')
     call results_addAttribute('DADF5_version_major',0)
-    call results_addAttribute('DADF5_version_minor',11)
+    call results_addAttribute('DADF5_version_minor',12)
     call results_addAttribute('DAMASK_version',DAMASKVERSION)
     call get_command(commandLine)
-    call results_addAttribute('Call',trim(commandLine))
+    call results_addAttribute('call',trim(commandLine))
-    call results_closeGroup(results_addGroup('mapping'))
+    call results_closeGroup(results_addGroup('cell_to'))
+    call results_addAttribute('description','mappings to place data in space','cell_to')
     call results_closeJobFile
   endif
 
@@ -105,12 +106,14 @@ subroutine results_addIncrement(inc,time)
 
   integer,       intent(in) :: inc
   real(pReal),   intent(in) :: time
+
   character(len=pStringLen) :: incChar
 
+
   write(incChar,'(i10)') inc
-  call results_closeGroup(results_addGroup(trim('inc'//trim(adjustl(incChar)))))
+  call results_closeGroup(results_addGroup(trim('increment_'//trim(adjustl(incChar)))))
-  call results_setLink(trim('inc'//trim(adjustl(incChar))),'current')
+  call results_setLink(trim('increment_'//trim(adjustl(incChar))),'current')
-  call results_addAttribute('time/s',time,trim('inc'//trim(adjustl(incChar))))
+  call results_addAttribute('t/s',time,trim('increment_'//trim(adjustl(incChar))))
 
 end subroutine results_addIncrement
 
@@ -133,6 +136,7 @@ integer(HID_T) function results_openGroup(groupName)
 
   character(len=*), intent(in) :: groupName
 
+
   results_openGroup = HDF5_openGroup(resultsFile,groupName)
 
 end function results_openGroup
@@ -145,6 +149,7 @@ integer(HID_T) function results_addGroup(groupName)
 
   character(len=*), intent(in) :: groupName
 
+
   results_addGroup = HDF5_addGroup(resultsFile,groupName)
 
 end function results_addGroup
@@ -157,6 +162,7 @@ subroutine results_closeGroup(group_id)
 
   integer(HID_T), intent(in) :: group_id
 
+
   call HDF5_closeGroup(group_id)
 
 end subroutine results_closeGroup
@@ -169,6 +175,7 @@ subroutine results_setLink(path,link)
 
   character(len=*), intent(in) :: path, link
 
+
   call HDF5_setLink(resultsFile,path,link)
 
 end subroutine results_setLink
@@ -181,6 +188,7 @@ subroutine results_addAttribute_str(attrLabel,attrValue,path)
   character(len=*), intent(in)           :: attrLabel, attrValue
   character(len=*), intent(in), optional :: path
 
+
   if (present(path)) then
     call HDF5_addAttribute(resultsFile,attrLabel, attrValue, path)
   else
@@ -199,6 +207,7 @@ subroutine results_addAttribute_int(attrLabel,attrValue,path)
   integer,          intent(in)           :: attrValue
   character(len=*), intent(in), optional :: path
 
+
   if (present(path)) then
     call HDF5_addAttribute(resultsFile,attrLabel, attrValue, path)
   else
@@ -217,6 +226,7 @@ subroutine results_addAttribute_real(attrLabel,attrValue,path)
   real(pReal),      intent(in)           :: attrValue
   character(len=*), intent(in), optional :: path
 
+
   if (present(path)) then
     call HDF5_addAttribute(resultsFile,attrLabel, attrValue, path)
   else
@@ -235,6 +245,7 @@ subroutine results_addAttribute_int_array(attrLabel,attrValue,path)
   integer,          intent(in), dimension(:) :: attrValue
   character(len=*), intent(in), optional     :: path
 
+
   if (present(path)) then
     call HDF5_addAttribute(resultsFile,attrLabel, attrValue, path)
   else
@@ -253,6 +264,7 @@ subroutine results_addAttribute_real_array(attrLabel,attrValue,path)
   real(pReal),      intent(in), dimension(:) :: attrValue
   character(len=*), intent(in), optional     :: path
 
+
   if (present(path)) then
     call HDF5_addAttribute(resultsFile,attrLabel, attrValue, path)
   else
@@ -270,6 +282,7 @@ subroutine results_removeLink(link)
   character(len=*), intent(in) :: link
   integer                      :: hdferr
 
+
   call h5ldelete_f(resultsFile,link, hdferr)
   if (hdferr < 0) call IO_error(1,ext_msg = 'results_removeLink: h5ldelete_soft_f ('//trim(link)//')')
 
@@ -277,7 +290,7 @@ end subroutine results_removeLink
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief stores a scalar dataset in a group
+!> @brief Store real scalar dataset with associated metadata.
 !--------------------------------------------------------------------------------------------------
 subroutine results_writeScalarDataset_real(group,dataset,label,description,SIunit)
 
@@ -287,24 +300,17 @@ subroutine results_writeScalarDataset_real(group,dataset,label,description,SIuni
 
   integer(HID_T) :: groupHandle
 
+
   groupHandle = results_openGroup(group)
-
   call HDF5_write(groupHandle,dataset,label)
-
+  call executionStamp(group//'/'//label,description,SIunit)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Description',description,label)
-  if (HDF5_objectExists(groupHandle,label) .and. present(SIunit)) &
-    call HDF5_addAttribute(groupHandle,'Unit',SIunit,label)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Created',now(),label)
   call HDF5_closeGroup(groupHandle)
 
 end subroutine results_writeScalarDataset_real
 
+
 !--------------------------------------------------------------------------------------------------
-!> @brief stores a vector dataset in a group
+!> @brief Store real vector dataset with associated metadata.
 !--------------------------------------------------------------------------------------------------
 subroutine results_writeVectorDataset_real(group,dataset,label,description,SIunit)
 
@@ -314,25 +320,18 @@ subroutine results_writeVectorDataset_real(group,dataset,label,description,SIuni
 
   integer(HID_T) :: groupHandle
 
+
   groupHandle = results_openGroup(group)
-
   call HDF5_write(groupHandle,dataset,label)
-
+  call executionStamp(group//'/'//label,description,SIunit)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Description',description,label)
-  if (HDF5_objectExists(groupHandle,label) .and. present(SIunit)) &
-    call HDF5_addAttribute(groupHandle,'Unit',SIunit,label)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Created',now(),label)
   call HDF5_closeGroup(groupHandle)
 
 end subroutine results_writeVectorDataset_real
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief stores a tensor dataset in a group
+!> @brief Store real tensor dataset with associated metadata.
+!> @details Data is transposed to compenstate transposed storage order.
 !--------------------------------------------------------------------------------------------------
 subroutine results_writeTensorDataset_real(group,dataset,label,description,SIunit,transposed)
 
@@ -353,35 +352,25 @@ subroutine results_writeTensorDataset_real(group,dataset,label,description,SIuni
     transposed_ = .true.
   endif
 
+  groupHandle = results_openGroup(group)
   if(transposed_) then
     if(size(dataset,1) /= size(dataset,2)) error stop 'transpose non-symmetric tensor'
     allocate(dataset_transposed,mold=dataset)
     do i=1,size(dataset_transposed,3)
       dataset_transposed(:,:,i) = transpose(dataset(:,:,i))
     enddo
-  else
-    allocate(dataset_transposed,source=dataset)
-  endif
-
-  groupHandle = results_openGroup(group)
-
     call HDF5_write(groupHandle,dataset_transposed,label)
-
+  else
-  if (HDF5_objectExists(groupHandle,label)) &
+    call HDF5_write(groupHandle,dataset,label)
-    call HDF5_addAttribute(groupHandle,'Description',description,label)
+  endif
-  if (HDF5_objectExists(groupHandle,label) .and. present(SIunit)) &
+  call executionStamp(group//'/'//label,description,SIunit)
-    call HDF5_addAttribute(groupHandle,'Unit',SIunit,label)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Created',now(),label)
   call HDF5_closeGroup(groupHandle)
 
 end subroutine results_writeTensorDataset_real
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief stores a vector dataset in a group
+!> @brief Store integer vector dataset with associated metadata.
 !--------------------------------------------------------------------------------------------------
 subroutine results_writeVectorDataset_int(group,dataset,label,description,SIunit)
 
@@ -391,25 +380,17 @@ subroutine results_writeVectorDataset_int(group,dataset,label,description,SIunit
 
   integer(HID_T) :: groupHandle
 
+
   groupHandle = results_openGroup(group)
-
   call HDF5_write(groupHandle,dataset,label)
-
+  call executionStamp(group//'/'//label,description,SIunit)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Description',description,label)
-  if (HDF5_objectExists(groupHandle,label) .and. present(SIunit)) &
-    call HDF5_addAttribute(groupHandle,'Unit',SIunit,label)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Created',now(),label)
   call HDF5_closeGroup(groupHandle)
 
 end subroutine results_writeVectorDataset_int
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief stores a tensor dataset in a group
+!> @brief Store integer tensor dataset with associated metadata.
 !--------------------------------------------------------------------------------------------------
 subroutine results_writeTensorDataset_int(group,dataset,label,description,SIunit)
 
@@ -419,20 +400,13 @@ subroutine results_writeTensorDataset_int(group,dataset,label,description,SIunit
 
   integer(HID_T) :: groupHandle
 
+
   groupHandle = results_openGroup(group)
-
   call HDF5_write(groupHandle,dataset,label)
-
+  call executionStamp(group//'/'//label,description,SIunit)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Description',description,label)
-  if (HDF5_objectExists(groupHandle,label) .and. present(SIunit)) &
-    call HDF5_addAttribute(groupHandle,'Unit',SIunit,label)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label)
-  if (HDF5_objectExists(groupHandle,label)) &
-    call HDF5_addAttribute(groupHandle,'Created',now(),label)
   call HDF5_closeGroup(groupHandle)
 
+
 end subroutine results_writeTensorDataset_int
 
 
@@ -458,8 +432,8 @@ subroutine results_mapping_phase(phaseAt,memberAtLocal,label)
   integer(HID_T) :: &
     loc_id, &                                                                                       !< identifier of group in file
     dtype_id, &                                                                                     !< identifier of compound data type
-    name_id, &                                                                                      !< identifier of name (string) in compound data type
+    label_id, &                                                                                     !< identifier of label (string) in compound data type
-    position_id, &                                                                                  !< identifier of position/index (integer) in compound data type
+    entry_id, &                                                                                     !< identifier of entry (integer) in compound data type
     dset_id, &
     memspace_id, &
     filespace_id, &
@@ -524,21 +498,21 @@ subroutine results_mapping_phase(phaseAt,memberAtLocal,label)
 
   call h5tcreate_f(H5T_COMPOUND_F, type_size_string + type_size_int, dtype_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt_id,hdferr)
+  call h5tinsert_f(dtype_id, 'label', 0_SIZE_T, dt_id,hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(dtype_id, "Position", type_size_string, H5T_NATIVE_INTEGER, hdferr)
+  call h5tinsert_f(dtype_id, 'entry', type_size_string, H5T_NATIVE_INTEGER, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
 !--------------------------------------------------------------------------------------------------
 ! create memory types for each component of the compound type
-  call h5tcreate_f(H5T_COMPOUND_F, type_size_string, name_id, hdferr)
+  call h5tcreate_f(H5T_COMPOUND_F, type_size_string, label_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt_id, hdferr)
+  call h5tinsert_f(label_id, 'label', 0_SIZE_T, dt_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call h5tcreate_f(H5T_COMPOUND_F, type_size_int, position_id, hdferr)
+  call h5tcreate_f(H5T_COMPOUND_F, type_size_int, entry_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
+  call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
   call h5tclose_f(dt_id, hdferr)
@@ -560,14 +534,14 @@ subroutine results_mapping_phase(phaseAt,memberAtLocal,label)
   call h5pset_preserve_f(plist_id, .true., hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  loc_id = results_openGroup('/mapping')
+  loc_id = results_openGroup('/cell_to')
   call h5dcreate_f(loc_id, 'phase', dtype_id, filespace_id, dset_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call h5dwrite_f(dset_id, name_id, reshape(label(pack(phaseAtMaterialpoint,.true.)),myShape), &
+  call h5dwrite_f(dset_id, label_id, reshape(label(pack(phaseAtMaterialpoint,.true.)),myShape), &
                   myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5dwrite_f(dset_id, position_id, reshape(pack(memberAtGlobal,.true.),myShape), &
+  call h5dwrite_f(dset_id, entry_id, reshape(pack(memberAtGlobal,.true.),myShape), &
                   myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
   if(hdferr < 0) error stop 'HDF5 error'
 
@@ -584,9 +558,11 @@ subroutine results_mapping_phase(phaseAt,memberAtLocal,label)
   if(hdferr < 0) error stop 'HDF5 error'
   call h5tclose_f(dtype_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tclose_f(name_id, hdferr)
+  call h5tclose_f(label_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tclose_f(position_id, hdferr)
+  call h5tclose_f(entry_id, hdferr)
+
+  call executionStamp('cell_to/phase','cell ID and constituent ID to phase results')
 
 end subroutine results_mapping_phase
 
@@ -613,8 +589,8 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
   integer(HID_T) :: &
     loc_id, &                                                                                       !< identifier of group in file
     dtype_id, &                                                                                     !< identifier of compound data type
-    name_id, &                                                                                      !< identifier of name (string) in compound data type
+    label_id, &                                                                                     !< identifier of label (string) in compound data type
-    position_id, &                                                                                  !< identifier of position/index (integer) in compound data type
+    entry_id, &                                                                                     !< identifier of entry (integer) in compound data type
     dset_id, &
     memspace_id, &
     filespace_id, &
@@ -680,21 +656,21 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
 
   call h5tcreate_f(H5T_COMPOUND_F, type_size_string + type_size_int, dtype_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt_id,hdferr)
+  call h5tinsert_f(dtype_id, 'label', 0_SIZE_T, dt_id,hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(dtype_id, "Position", type_size_string, H5T_NATIVE_INTEGER, hdferr)
+  call h5tinsert_f(dtype_id, 'entry', type_size_string, H5T_NATIVE_INTEGER, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
 !--------------------------------------------------------------------------------------------------
 ! create memory types for each component of the compound type
-  call h5tcreate_f(H5T_COMPOUND_F, type_size_string, name_id, hdferr)
+  call h5tcreate_f(H5T_COMPOUND_F, type_size_string, label_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt_id, hdferr)
+  call h5tinsert_f(label_id, 'label', 0_SIZE_T, dt_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call h5tcreate_f(H5T_COMPOUND_F, type_size_int, position_id, hdferr)
+  call h5tcreate_f(H5T_COMPOUND_F, type_size_int, entry_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
+  call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
   call h5tclose_f(dt_id, hdferr)
@@ -716,14 +692,14 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
   call h5pset_preserve_f(plist_id, .true., hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  loc_id = results_openGroup('/mapping')
+  loc_id = results_openGroup('/cell_to')
   call h5dcreate_f(loc_id, 'homogenization', dtype_id, filespace_id, dset_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call h5dwrite_f(dset_id, name_id, reshape(label(pack(homogenizationAtMaterialpoint,.true.)),myShape), &
+  call h5dwrite_f(dset_id, label_id, reshape(label(pack(homogenizationAtMaterialpoint,.true.)),myShape), &
                   myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5dwrite_f(dset_id, position_id, reshape(pack(memberAtGlobal,.true.),myShape), &
+  call h5dwrite_f(dset_id, entry_id, reshape(pack(memberAtGlobal,.true.),myShape), &
                   myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
   if(hdferr < 0) error stop 'HDF5 error'
 
@@ -740,26 +716,52 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
   if(hdferr < 0) error stop 'HDF5 error'
   call h5tclose_f(dtype_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tclose_f(name_id, hdferr)
+  call h5tclose_f(label_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tclose_f(position_id, hdferr)
+  call h5tclose_f(entry_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
+  call executionStamp('cell_to/homogenization','cell ID to homogenization results')
+
 end subroutine results_mapping_homogenization
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief current date and time (including time zone information)
+!> @brief Add default information to a dataset.
+!--------------------------------------------------------------------------------------------------
+subroutine executionStamp(path,description,SIunit)
+
+
+  character(len=*), intent(in)           :: path,description
+  character(len=*), intent(in), optional :: SIunit
+
+
+  if (HDF5_objectExists(resultsFile,path)) &
+    call HDF5_addAttribute(resultsFile,'description',description,path)
+  if (HDF5_objectExists(resultsFile,path) .and. present(SIunit)) &
+    call HDF5_addAttribute(resultsFile,'unit',SIunit,path)
+  if (HDF5_objectExists(resultsFile,path)) &
+    call HDF5_addAttribute(resultsFile,'creator','DAMASK '//DAMASKVERSION,path)
+  if (HDF5_objectExists(resultsFile,path)) &
+    call HDF5_addAttribute(resultsFile,'created',now(),path)
+
+end subroutine executionStamp
+
+
+!--------------------------------------------------------------------------------------------------
+!> @brief Return current date and time (including time zone information).
 !--------------------------------------------------------------------------------------------------
 character(len=24) function now()
 
   character(len=5)      :: zone
   integer, dimension(8) :: values
 
+
   call date_and_time(values=values,zone=zone)
   write(now,'(i4.4,5(a,i2.2),a)') &
     values(1),'-',values(2),'-',values(3),' ',values(5),':',values(6),':',values(7),zone
 
 end function now
 
+
 end module results

src/rotations.f90

@@ -105,7 +105,7 @@ subroutine rotations_init
 
   print'(/,a)', ' <<<+-  rotations init  -+>>>'; flush(IO_STDOUT)
 
-  print*, 'Rowenhorst et al., Modelling and Simulation in Materials Science and Engineering 23:083501, 2015'
+  print*, 'D. Rowenhorst et al., Modelling and Simulation in Materials Science and Engineering 23:083501, 2015'
   print*, 'https://doi.org/10.1088/0965-0393/23/8/083501'
 
   call selfTest