Merge remote-tracking branch 'origin/general-N_constituents' into vtr-only

.gitattributes

@@ -8,6 +8,7 @@
 *.jpg binary
 *.hdf5 binary
 *.pdf binary
+*.dream3d binary
 
 # ignore files from MSC.Marc in language statistics
 installation/mods_MarcMentat/20*/*  linguist-vendored

.gitlab-ci.yml

@@ -193,6 +193,8 @@ grid_mech_compile_Intel:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
     - cp -r grid_mech_compile grid_mech_compile_Intel
     - grid_mech_compile_Intel/test.py
+    - cd pytest
+    - pytest -k 'compile and grid'
   except:
     - master
     - release
@@ -203,6 +205,8 @@ Compile_FEM_Intel:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
     - cp -r FEM_compile FEM_compile_Intel
     - FEM_compile_Intel/test.py
+    - cd pytest
+    - pytest -k 'compile and mesh'
   except:
     - master
     - release
@@ -213,6 +217,8 @@ grid_mech_compile_GNU:
     - module load $GNUCompiler $MPICH_GNU $PETSc_MPICH_GNU
     - cp -r grid_mech_compile grid_mech_compile_GNU
     - grid_mech_compile_GNU/test.py
+    - cd pytest
+    - pytest -k 'compile and grid'
   except:
     - master
     - release
@@ -223,6 +229,8 @@ Compile_FEM_GNU:
     - module load $GNUCompiler $MPICH_GNU $PETSc_MPICH_GNU
     - cp -r FEM_compile FEM_compile_GNU
     - FEM_compile_GNU/test.py
+    - cd pytest
+    - pytest -k 'compile and mesh'
   except:
     - master
     - release
@@ -244,7 +252,7 @@ Pytest_grid:
   script:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
     - cd pytest
-    - pytest
+    - pytest -m 'not compile'
   except:
     - master
     - release
@@ -306,6 +314,8 @@ Marc_compileIfort:
   script:
     - module load $IntelMarc $HDF5Marc $MSC
     - Marc_compileIfort/test.py
+    - cd pytest
+    - pytest -k 'compile and Marc'
   except:
     - master
     - release

VERSION

@@ -1 +1 @@
-v3.0.0-alpha-452-gd3f068cd7
+v3.0.0-alpha-502-g8ab405e5d

examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Ferrite.config

@@ -1,21 +0,0 @@
-# Tasan et.al. 2015 Acta Materalia
-# Tasan et.al. 2015 International Journal of Plasticity
-# Diehl et.al. 2015 Meccanica
-[BCC-Ferrite]
-
-elasticity              hooke
-plasticity              phenopowerlaw
-
-lattice_structure       bcc
-Nslip                   12  12                  # per family
-Ntwin                    0                      # per family
-c11                     233.3e9
-c12                     135.5e9
-c44                     118.0e9
-gdot0_slip              0.001
-n_slip                  20
-tau0_slip                95.e6  97.e6           # per family, optimization long simplex 109
-tausat_slip             222.e6 412.7e6          # per family, optimization long simplex 109
-h0_slipslip             1000.0e6
-interaction_slipslip    1 1 1.4 1.4 1.4 1.4
-a_slip                 2.0

examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Ferrite.yaml

@@ -0,0 +1,16 @@
+# Tasan et.al. 2015 Acta Materalia
+# Tasan et.al. 2015 International Journal of Plasticity
+# Diehl et.al. 2015 Meccanica
+Ferrite:
+  elasticity: {C_11: 233.3e9, C_12: 135.5e9, C_44: 118.0e9, type: hooke}
+  lattice: bcc
+  plasticity:
+    N_sl: [12, 12]
+    a_sl: 2.0
+    dot_gamma_0_sl: 0.001
+    h_0_sl_sl: 1000.0e6
+    h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4]
+    n_sl: 20
+    type: phenopowerlaw
+    xi_0_sl: [95.e6, 96.e6]
+    xi_inf_sl: [222.e6, 412.7e6]

examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.config

@@ -1,21 +0,0 @@
-# Tasan et.al. 2015 Acta Materalia
-# Tasan et.al. 2015 International Journal of Plasticity
-# Diehl et.al. 2015 Meccanica
-[BCC-Martensite]
-
-elasticity              hooke
-plasticity              phenopowerlaw
-
-lattice_structure       bcc
-Nslip                   12  12                  # per family
-Ntwin                    0                      # per family
-c11                     417.4e9
-c12                     242.4e9
-c44                     211.1e9
-gdot0_slip              0.001
-n_slip                  20
-tau0_slip               405.8e6  456.7e6        # per family
-tausat_slip             872.9e6  971.2e6        # per family
-h0_slipslip             563.0e9
-interaction_slipslip    1 1 1.4 1.4 1.4 1.4
-a_slip                 2.0

examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.yaml

@@ -0,0 +1,16 @@
+# Tasan et.al. 2015 Acta Materalia
+# Tasan et.al. 2015 International Journal of Plasticity
+# Diehl et.al. 2015 Meccanica
+Martensite:
+  elasticity: {C_11: 417.4e9, C_12: 242.4e9, C_44: 211.1e9, type: hooke}
+  lattice: bcc
+  plasticity:
+    N_sl: [12, 12]
+    a_sl: 2.0
+    dot_gamma_0_sl: 0.001
+    h_0_sl_sl: 563.0e9
+    h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4]
+    n_sl: 20
+    type: phenopowerlaw
+    xi_0_sl: [405.8e6, 456.7e6]
+    xi_inf_sl: [872.9e6, 971.2e6]

examples/SpectralMethod/Polycrystal/material.yaml

@@ -1,3 +1,4 @@
+---
 homogenization:
   SX:
     N_constituents: 1

processing/post/addGaussian.py

@@ -1,76 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-from io import StringIO
-from optparse import OptionParser
-
-from scipy import ndimage
-
-import damask
-
-
-scriptName = os.path.splitext(os.path.basename(__file__))[0]
-scriptID   = ' '.join([scriptName,damask.version])
-
-
-# --------------------------------------------------------------------
-#                                MAIN
-# --------------------------------------------------------------------
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [ASCIItable(s)]', description = """
-Add column(s) containing Gaussian filtered values of requested column(s).
-Operates on periodic and non-periodic ordered three-dimensional data sets.
-For details see scipy.ndimage documentation.
-
-""", version = scriptID)
-
-parser.add_option('-p','--pos','--periodiccellcenter',
-                  dest = 'pos',
-                  type = 'string', metavar = 'string',
-                  help = 'label of coordinates [%default]')
-parser.add_option('-s','--scalar',
-                  dest = 'labels',
-                  action = 'extend', metavar = '<string LIST>',
-                  help = 'label(s) of scalar field values')
-parser.add_option('-o','--order',
-                  dest = 'order',
-                  type = int,
-                  metavar = 'int',
-                  help = 'order of the filter [%default]')
-parser.add_option('--sigma',
-                  dest = 'sigma',
-                  type = float,
-                  metavar = 'float',
-                  help = 'standard deviation [%default]')
-parser.add_option('--periodic',
-                  dest = 'periodic',
-                  action = 'store_true',
-                  help = 'assume periodic grain structure')
-
-
-
-parser.set_defaults(pos = 'pos',
-                    order = 0,
-                    sigma = 1,
-                   )
-
-(options,filenames) = parser.parse_args()
-if filenames == []: filenames = [None]
-
-if options.labels is None: parser.error('no data column specified.')
-
-for name in filenames:
-    damask.util.report(scriptName,name)
-
-    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    damask.grid_filters.coord0_check(table.get(options.pos))
-
-    for label in options.labels:
-        table = table.add('Gauss{}({})'.format(options.sigma,label),
-                          ndimage.filters.gaussian_filter(table.get(label).reshape(-1),
-                                                          options.sigma,options.order,
-                                                          mode = 'wrap' if options.periodic else 'nearest'),
-                          scriptID+' '+' '.join(sys.argv[1:]))
-
-    table.save((sys.stdout if name is None else name), legacy=True)

processing/pre/geom_fromDREAM3D.py

@@ -1,12 +1,8 @@
 #!/usr/bin/env python3
 
 import os
-import sys
 from optparse import OptionParser
 
-import h5py
-import numpy as np
-
 import damask
 
 
@@ -64,88 +60,12 @@ parser.set_defaults(pointwise      = 'CellData',
 if options.basegroup is None:
   parser.error('No base group selected')
 
-rootDir ='DataContainers'
-
-
 if filenames == []: parser.error('no input file specified.')
 
 for name in filenames:
     damask.util.report(scriptName,name)
 
-  errors = []
+    geom = damask.Geom.load_DREAM3D(name,options.basegroup,options.pointwise)
-
-  inFile = h5py.File(name, 'r')
-  group_geom = os.path.join(rootDir,options.basegroup,'_SIMPL_GEOMETRY')
-  try:
-    size   = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
-           * inFile[os.path.join(group_geom,'SPACING')][...]
-    grid   = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
-    origin = inFile[os.path.join(group_geom,'ORIGIN')][...]
-  except KeyError:
-    errors.append('Geometry data ({}) not found'.format(group_geom))
-
-
-  group_pointwise = os.path.join(rootDir,options.basegroup,options.pointwise)
-  if options.average is None:
-    label = 'Point'
-
-    dataset = os.path.join(group_pointwise,options.quaternion)
-    try:
-      quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
-      rot   = [damask.Rotation.from_quaternion(q,True,P=+1) for q in quats]
-    except KeyError:
-      errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
-
-    dataset = os.path.join(group_pointwise,options.phase)
-    try:
-      phase = np.reshape(inFile[dataset][...],(np.product(grid)))
-    except KeyError:
-      errors.append('Pointwise phase data ({}) not readable'.format(dataset))
-
-    microstructure = np.arange(1,np.product(grid)+1,dtype=int).reshape(grid,order='F')
-
-
-  else:
-    label = 'Grain'
-
-    dataset = os.path.join(group_pointwise,options.microstructure)
-    try:
-      microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0))               # convert from C ordering
-    except KeyError:
-      errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
-
-    group_average = os.path.join(rootDir,options.basegroup,options.average)
-
-    dataset = os.path.join(group_average,options.quaternion)
-    try:
-      rot = [damask.Rotation.from_quaternion(q,True,P=+1) for q in inFile[dataset][...][1:]]        # skip first entry (unindexed)
-    except KeyError:
-      errors.append('Average orientation data ({}) not readable'.format(dataset))
-
-    dataset = os.path.join(group_average,options.phase)
-    try:
-      phase = [i[0] for i in inFile[dataset][...]][1:]                                              # skip first entry (unindexed)
-    except KeyError:
-      errors.append('Average phase data ({}) not readable'.format(dataset))
-
-  if errors != []:
-    damask.util.croak(errors)
-    continue
-
-  config_header = ['<texture>']
-  for i in range(np.nanmax(microstructure)):
-    config_header += ['[{}{}]'.format(label,i+1),
-                      '(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*rot[i].as_Eulers(degrees = True)),
-                     ]
-  config_header += ['<microstructure>']
-  for i in range(np.nanmax(microstructure)):
-    config_header += ['[{}{}]'.format(label,i+1),
-                      '(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(phase[i],i+1),
-                      ]
-
-  header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
-         + config_header
-  geom = damask.Geom(microstructure,size,origin,comments=header)
     damask.util.croak(geom)
 
     geom.save_ASCII(os.path.splitext(name)[0]+'.geom')

processing/pre/geom_fromTable.py

@@ -2,11 +2,8 @@
 
 import os
 import sys
-from io import StringIO
 from optparse import OptionParser
 
-import numpy as np
-
 import damask
 
 
@@ -40,64 +37,21 @@ parser.add_option('-q', '--quaternion',
                   dest = 'quaternion',
                   type = 'string', metavar='string',
                   help = 'quaternion label')
-parser.add_option('--axes',
-                  dest = 'axes',
-                  type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
-                  help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]')
 
-
+parser.set_defaults(pos= 'pos')
-parser.set_defaults(pos            = 'pos',
-                   )
 
 (options,filenames) = parser.parse_args()
 if filenames == []: filenames = [None]
 
-if np.sum([options.quaternion     is not None,
-           options.microstructure is not None]) != 1:
-  parser.error('need either microstructure or quaternion (and optionally phase) as input.')
-if options.microstructure is not None and options.phase is not None:
-  parser.error('need either microstructure or phase (and mandatory quaternion) as input.')
-if options.axes is not None and not set(options.axes).issubset(set(['x','+x','-x','y','+y','-y','z','+z','-z'])):
-  parser.error('invalid axes {} {} {}.'.format(*options.axes))
-
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    labels = []
-    table.sort_by(['{}_{}'.format(i,options.pos) for i in range(3,0,-1)])                           # x fast, y slow
+    for l in [options.quaternion,options.phase,options.microstructure]:
-    grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
+        if l is not None: labels.append(l)
 
-    config_header  = table.comments
+    t = damask.Table.load(name)
-
+    geom = damask.Geom.from_table(t,options.pos,labels)
-    if   options.microstructure:
-        microstructure = table.get(options.microstructure).reshape(grid,order='F')
-
-    elif options.quaternion:
-        q     = table.get(options.quaternion)
-        phase = table.get(options.phase).astype(int) if options.phase else \
-                np.ones((table.data.shape[0],1),dtype=int)
-
-        unique,unique_inverse = np.unique(np.hstack((q,phase)),return_inverse=True,axis=0)
-        microstructure = unique_inverse.reshape(grid,order='F') + 1
-
-        config_header = ['<texture>']
-        for i,data in enumerate(unique):
-            ori = damask.Rotation(data[0:4])
-            config_header += ['[Grain{}]'.format(i+1),
-                              '(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*ori.as_Eulers(degrees = True)),
-                             ]
-            if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)]
-
-        config_header += ['<microstructure>']
-        for i,data in enumerate(unique):
-            config_header += ['[Grain{}]'.format(i+1),
-                              '(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(int(data[4]),i+1),
-                             ]
-
-    header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
-           + config_header
-    geom = damask.Geom(microstructure,size,origin,
-                       comments=header)
     damask.util.croak(geom)
 
     geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom')

python/damask/__init__.py

@@ -10,20 +10,21 @@ with open(_Path(__file__).parent/_Path('VERSION')) as _f:
 # make classes directly accessible as damask.Class
 from ._environment import Environment as _ # noqa
 environment = _()
-from ._table       import Table            # noqa
-from ._vtk         import VTK              # noqa
-from ._colormap    import Colormap         # noqa
-from ._rotation    import Rotation         # noqa
-from ._lattice     import Symmetry, Lattice# noqa
-from ._orientation import Orientation      # noqa
-from ._result      import Result           # noqa
-from ._geom        import Geom             # noqa
-from ._material    import Material         # noqa
-from .             import solver           # noqa
 from .                 import util             # noqa
 from .                 import seeds            # noqa
-from .             import grid_filters     # noqa
 from .                 import mechanics        # noqa
+from .                 import solver           # noqa
+from .                 import grid_filters     # noqa
+from ._lattice         import Symmetry, Lattice# noqa
+from ._table           import Table            # noqa
+from ._rotation        import Rotation         # noqa
+from ._vtk             import VTK              # noqa
+from ._colormap        import Colormap         # noqa
+from ._orientation     import Orientation      # noqa
+from ._config          import Config           # noqa
+from ._configmaterial  import ConfigMaterial   # noqa
+from ._geom            import Geom             # noqa
+from ._result          import Result           # noqa
 
 
 

python/damask/_config.py

@@ -0,0 +1,80 @@
+from io import StringIO
+import abc
+
+import yaml
+
+class NiceDumper(yaml.SafeDumper):
+    """Make YAML readable for humans."""
+
+    def write_line_break(self, data=None):
+        super().write_line_break(data)
+
+        if len(self.indents) == 1:
+            super().write_line_break()
+
+    def increase_indent(self, flow=False, indentless=False):
+        return super().increase_indent(flow, False)
+
+
+class Config(dict):
+    """YAML-based configuration."""
+
+    def __repr__(self):
+        """Show as in file."""
+        output = StringIO()
+        self.save(output)
+        output.seek(0)
+        return ''.join(output.readlines())
+
+    @classmethod
+    def load(cls,fname):
+        """
+        Load from yaml file.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path
+            Filename or file for writing.
+
+        """
+        try:
+            fhandle = open(fname)
+        except TypeError:
+            fhandle = fname
+        return cls(yaml.safe_load(fhandle))
+
+    def save(self,fname,**kwargs):
+        """
+        Save to yaml file.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path
+            Filename or file for writing.
+        **kwargs : dict
+            Keyword arguments parsed to yaml.dump.
+
+        """
+        try:
+            fhandle = open(fname,'w')
+        except TypeError:
+            fhandle = fname
+
+        if 'width' not in kwargs:
+            kwargs['width'] = 256
+        if 'default_flow_style' not in kwargs:
+            kwargs['default_flow_style'] = None
+        fhandle.write(yaml.dump(dict(self),Dumper=NiceDumper,**kwargs))
+
+
+    @property
+    @abc.abstractmethod
+    def is_complete(self):
+        """Check for completeness."""
+        pass
+
+    @property
+    @abc.abstractmethod
+    def is_valid(self):
+        """Check for valid file layout."""
+        pass

python/damask/_configmaterial.py

@@ -0,0 +1,299 @@
+import copy
+
+import numpy as np
+
+from . import grid_filters
+from . import Config
+from . import Lattice
+from . import Rotation
+
+class ConfigMaterial(Config):
+    """Material configuration."""
+
+    def save(self,fname='material.yaml',**kwargs):
+        """
+        Save to yaml file.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path, optional
+            Filename or file for writing. Defaults to 'material.yaml'.
+        **kwargs
+            Keyword arguments parsed to yaml.dump.
+
+        """
+        super().save(fname,**kwargs)
+
+
+    @staticmethod
+    def from_table(table,coordinates=None,constituents={},**kwargs):
+        """
+        Load from an ASCII table.
+
+        Parameters
+        ----------
+        table : damask.Table
+            Table that contains material information.
+        coordinates : str, optional
+            Label of spatial coordiates. Used for sorting and performing a
+            sanity check. Default to None, in which case no sorting or checking is
+            peformed.
+        constituents : dict, optional
+            Entries for 'constituents'. The key is the name and the value specifies
+            the label of the data column in the table
+        **kwargs
+            Keyword arguments where the key is the name and  the value specifies
+            the label of the data column in the table
+
+        Examples
+        --------
+        >>> import damask
+        >>> import damask.ConfigMaterial as cm
+        >>> t = damask.Table.load('small.txt')
+        >>> t
+            pos  pos  pos   qu   qu    qu    qu   phase    homog
+        0    0    0    0  0.19  0.8   0.24 -0.51  Aluminum SX
+        1    1    0    0  0.8   0.19  0.24 -0.51  Steel    SX
+        >>> cm.from_table(t,'pos',{'O':'qu','phase':'phase'},homogenization='homog')
+        material:
+          - constituents:
+              - O: [0.19, 0.8, 0.24, -0.51]
+                fraction: 1.0
+                phase: Aluminum
+            homogenization: SX
+          - constituents:
+              - O: [0.8, 0.19, 0.24, -0.51]
+                fraction: 1.0
+                phase: Steel
+            homogenization: SX
+
+        """
+        if coordinates is not None:
+            t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
+            grid_filters.coord0_check(t.get(coordinates))
+        else:
+            t = table
+
+        constituents_ = {k:t.get(v) for k,v in constituents.items()}
+        kwargs_       = {k:t.get(v) for k,v in kwargs.items()}
+
+        _,idx = np.unique(np.hstack(list({**constituents_,**kwargs_}.values())),return_index=True,axis=0)
+
+        constituents_ = {k:v[idx].squeeze() for k,v in constituents_.items()}
+        kwargs_       = {k:v[idx].squeeze() for k,v in kwargs_.items()}
+
+        return ConfigMaterial().material_add(constituents_,**kwargs_)
+
+
+    @property
+    def is_complete(self):
+        """Check for completeness."""
+        ok = True
+        for top_level in ['homogenization','phase','material']:
+            # ToDo: With python 3.8 as prerequisite we can shorten with :=
+            ok &= top_level in self
+            if top_level not in self: print(f'{top_level} entry missing')
+
+        if ok:
+           ok &= len(self['material']) > 0
+           if len(self['material']) < 1: print('Incomplete material definition')
+
+        if ok:
+            homogenization = set()
+            phase          = set()
+            for i,v in enumerate(self['material']):
+                if 'homogenization' in v:
+                    homogenization.add(v['homogenization'])
+                else:
+                    print(f'No homogenization specified in material {i}')
+                    ok = False
+
+                if 'constituents' in v:
+                    for ii,vv in enumerate(v['constituents']):
+                        if 'O' not in vv:
+                            print('No orientation specified in constituent {ii} of material {i}')
+                            ok = False
+                        if 'phase' in vv:
+                            phase.add(vv['phase'])
+                        else:
+                            print(f'No phase specified in constituent {ii} of material {i}')
+                            ok = False
+
+            for k,v in self['phase'].items():
+                if 'lattice' not in v:
+                    print(f'No lattice specified in phase {k}')
+                    ok = False
+
+            for k,v in self['homogenization'].items():
+                if 'N_constituents' not in v:
+                    print(f'No. of constituents not specified in homogenization {k}')
+                    ok = False
+
+            if phase - set(self['phase']):
+                print(f'Phase(s) {phase-set(self["phase"])} missing')
+                ok = False
+            if homogenization - set(self['homogenization']):
+                print(f'Homogenization(s) {homogenization-set(self["homogenization"])} missing')
+                ok = False
+
+        return ok
+
+
+    @property
+    def is_valid(self):
+        """Check for valid file layout."""
+        ok = True
+
+        if 'phase' in self:
+            for k,v in self['phase'].items():
+                if 'lattice' in v:
+                    try:
+                        Lattice(v['lattice'])
+                    except KeyError:
+                        s = v['lattice']
+                        print(f"Invalid lattice: '{s}' in phase '{k}'")
+                        ok = False
+
+        if 'material' in self:
+            for i,v in enumerate(self['material']):
+                if 'constituents' in v:
+                    f = 0.0
+                    for c in v['constituents']:
+                        f+= float(c['fraction'])
+                        if 'O' in c:
+                            try:
+                                Rotation.from_quaternion(c['O'])
+                            except ValueError:
+                                o = c['O']
+                                print(f"Invalid orientation: '{o}' in material '{i}'")
+                                ok = False
+                    if not np.isclose(f,1.0):
+                        print(f"Invalid total fraction '{f}' in material '{i}'")
+                        ok = False
+
+        return ok
+
+
+    def material_rename_phase(self,mapping,ID=None,constituent=None):
+        """
+        Change phase name in material.
+
+        Parameters
+        ----------
+        mapping: dictionary
+            Mapping from old name to new name
+        ID: list of ints, optional
+            Limit renaming to selected material IDs.
+        constituent: list of ints, optional
+            Limit renaming to selected constituents.
+
+        """
+        dup = copy.deepcopy(self)
+        for i,m in enumerate(dup['material']):
+            if ID and i not in ID: continue
+            for c in m['constituents']:
+                if constituent is not None and c not in constituent: continue
+                try:
+                    c['phase'] = mapping[c['phase']]
+                except KeyError:
+                    continue
+        return dup
+
+
+    def material_rename_homogenization(self,mapping,ID=None):
+        """
+        Change homogenization name in material.
+
+        Parameters
+        ----------
+        mapping: dictionary
+            Mapping from old name to new name
+        ID: list of ints, optional
+            Limit renaming to selected homogenization IDs.
+
+        """
+        dup = copy.deepcopy(self)
+        for i,m in enumerate(dup['material']):
+            if ID and i not in ID: continue
+            try:
+                m['homogenization'] = mapping[m['homogenization']]
+            except KeyError:
+                continue
+        return dup
+
+
+    def material_add(self,constituents,**kwargs):
+        """
+        Add material entries.
+
+        Parameters
+        ----------
+        constituents : dict
+            Entries for 'constituents'. The key is the name and the value specifies
+            the label of the data column in the table
+        **kwargs
+            Keyword arguments where the key is the name and  the value specifies
+            the label of the data column in the table
+
+        Examples
+        --------
+        >>> import damask
+        >>> m = damask.ConfigMaterial()
+        >>> O = damask.Rotation.from_random(3).as_quaternion()
+        >>> phase = ['Aluminum','Steel','Aluminum']
+        >>> m.material_add(constituents={'phase':phase,'O':O},homogenization='SX')
+        material:
+          - constituents:
+              - O: [0.577764, -0.146299, -0.617669, 0.513010]
+                fraction: 1.0
+                phase: Aluminum
+            homogenization: SX
+          - constituents:
+              - O: [0.184176, 0.340305, 0.737247, 0.553840]
+                fraction: 1.0
+                phase: Steel
+            homogenization: SX
+          - constituents:
+              - O: [0.0886257, -0.144848, 0.615674, -0.769487]
+                fraction: 1.0
+                phase: Aluminum
+            homogenization: SX
+
+        """
+        c = [{'constituents':u} for u in ConfigMaterial._constituents(**constituents)]
+        for k,v in kwargs.items():
+            if hasattr(v,'__len__') and not isinstance(v,str):
+                if len(v) != len(c):
+                    raise ValueError('len mismatch 1')
+                for i,vv in enumerate(v):
+                    c[i][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
+            else:
+                for i in range(len(c)):
+                    c[i][k] = v
+        dup = copy.deepcopy(self)
+        if 'material' not in dup: dup['material'] = []
+        dup['material'] +=c
+
+        return dup
+
+
+    @staticmethod
+    def _constituents(N=1,**kwargs):
+        """Construct list of constituents."""
+        for v in kwargs.values():
+            if hasattr(v,'__len__') and not isinstance(v,str): N_material = len(v)
+
+        if N == 1:
+            m = [[{'fraction':1.0}] for _ in range(N_material)]
+            for k,v in kwargs.items():
+                if hasattr(v,'__len__') and not isinstance(v,str):
+                    if len(v) != N_material:
+                        raise ValueError('len mismatch 2')
+                    for i,vv in enumerate(np.array(v)):
+                        m[i][0][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
+                else:
+                    for i in range(N_material):
+                        m[i][0][k] = v
+            return m
+        else:
+            raise NotImplementedError

python/damask/_geom.py

@@ -1,15 +1,17 @@
 import copy
 import multiprocessing as mp
 from functools import partial
+from os import path
 
 import numpy as np
+import h5py
 from scipy import ndimage,spatial
 
 from . import environment
-from . import Rotation
 from . import VTK
 from . import util
 from . import grid_filters
+from . import Rotation
 
 
 class Geom:
@@ -207,6 +209,68 @@ class Geom:
         return Geom(material.reshape(grid,order='F'),size,origin,comments)
 
 
+
+    @staticmethod
+    def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
+        """
+        Load a DREAM.3D file.
+
+        Parameters
+        ----------
+        fname : str
+            Filename of the DREAM.3D file
+        base_group : str
+            Name of the group (folder) below 'DataContainers'. For example
+            'SyntheticVolumeDataContainer'.
+        point_data : str, optional
+            Name of the group (folder) containing the point wise material data,
+            for example 'CellData'. Defaults to None, in which case points consecutively numbered.
+        material : str, optional
+            Name of the dataset containing the material ID. Defaults to
+            'FeatureIds'.
+
+        """
+        root_dir ='DataContainers'
+        f = h5py.File(fname, 'r')
+        g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
+        size   = f[path.join(g,'DIMENSIONS')][()] * f[path.join(g,'SPACING')][()]
+        grid   = f[path.join(g,'DIMENSIONS')][()]
+        origin = f[path.join(g,'ORIGIN')][()]
+        group_pointwise = path.join(root_dir,base_group,point_data)
+
+        ma = np.arange(1,np.product(grid)+1,dtype=int) if point_data is None else \
+             np.reshape(f[path.join(group_pointwise,material)],grid.prod())
+
+        return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','load_DREAM3D'))
+
+
+    @staticmethod
+    def from_table(table,coordinates,labels):
+        """
+        Load an ASCII table.
+
+        Parameters
+        ----------
+        table : damask.Table
+            Table that contains material information.
+        coordinates : str
+            Label of the column containing the spatial coordinates.
+        labels : str or list of str
+            Label(s) of the columns containing the material definition.
+            Each unique combintation of values results in a material.
+
+        """
+        t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
+
+        grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(t.get(coordinates))
+
+        labels_ = [labels] if isinstance(labels,str) else labels
+        _,unique_inverse = np.unique(np.hstack([t.get(l) for l in labels_]),return_inverse=True,axis=0)
+        ma = unique_inverse.reshape(grid,order='F') + 1
+
+        return Geom(ma,size,origin,util.execution_stamp('Geom','from_table'))
+
+
     @staticmethod
     def _find_closest_seed(seeds, weights, point):
         return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
@@ -399,7 +463,7 @@ class Geom:
 
     def save(self,fname,compress=True):
         """
-        Generate vtk rectilinear grid.
+        Store as vtk rectilinear grid.
 
         Parameters
         ----------
@@ -489,7 +553,7 @@ class Geom:
         coords_rot = R.broadcast_to(tuple(self.grid))@coords
 
         with np.errstate(all='ignore'):
-            mask = np.where(np.sum(np.power(coords_rot/r,2.0**exponent),axis=-1) > 1.0,True,False)
+            mask = np.sum(np.power(coords_rot/r,2.0**np.array(exponent)),axis=-1) > 1.0
 
         if periodic:                                                                                # translate back to center
             mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))

python/damask/_material.py

@@ -1,193 +0,0 @@
-from io import StringIO
-import copy
-
-import yaml
-import numpy as np
-
-from . import Lattice
-from . import Rotation
-
-class NiceDumper(yaml.SafeDumper):
-    """Make YAML readable for humans."""
-
-    def write_line_break(self, data=None):
-        super().write_line_break(data)
-
-        if len(self.indents) == 1:
-            super().write_line_break()
-
-    def increase_indent(self, flow=False, indentless=False):
-        return super().increase_indent(flow, False)
-
-
-class Material(dict):
-    """Material configuration."""
-
-    def __repr__(self):
-        """Show as in file."""
-        output = StringIO()
-        self.save(output)
-        output.seek(0)
-        return ''.join(output.readlines())
-
-    @staticmethod
-    def load(fname):
-        """Load from yaml file."""
-        try:
-            fhandle = open(fname)
-        except TypeError:
-            fhandle = fname
-        return Material(yaml.safe_load(fhandle))
-
-    def save(self,fname='material.yaml'):
-        """
-        Save to yaml file.
-
-        Parameters
-        ----------
-        fname : file, str, or pathlib.Path
-            Filename or file for reading.
-
-        """
-        try:
-            fhandle = open(fname,'w')
-        except TypeError:
-            fhandle = fname
-        fhandle.write(yaml.dump(dict(self),width=256,default_flow_style=None,Dumper=NiceDumper))
-
-
-    @property
-    def is_complete(self):
-        """Check for completeness."""
-        ok = True
-        for top_level in ['homogenization','phase','microstructure']:
-            # ToDo: With python 3.8 as prerequisite we can shorten with :=
-            ok &= top_level in self
-            if top_level not in self: print(f'{top_level} entry missing')
-
-        if ok:
-           ok &= len(self['microstructure']) > 0
-           if len(self['microstructure']) < 1: print('Incomplete microstructure definition')
-
-        if ok:
-            homogenization = set()
-            phase          = set()
-            for i,v in enumerate(self['microstructure']):
-                if 'homogenization' in v:
-                    homogenization.add(v['homogenization'])
-                else:
-                    print(f'No homogenization specified in microstructure {i}')
-                    ok = False
-
-                if 'constituents' in v:
-                    for ii,vv in enumerate(v['constituents']):
-                        if 'orientation' not in vv:
-                            print('No orientation specified in constituent {ii} of microstructure {i}')
-                            ok = False
-                        if 'phase' in vv:
-                            phase.add(vv['phase'])
-                        else:
-                            print(f'No phase specified in constituent {ii} of microstructure {i}')
-                            ok = False
-
-            for k,v in self['phase'].items():
-                if 'lattice' not in v:
-                    print(f'No lattice specified in phase {k}')
-                    ok = False
-
-            #for k,v in self['homogenization'].items():
-            #    if 'N_constituents' not in v:
-            #        print(f'No. of constituents not specified in homogenization {k}'}
-            #        ok = False
-
-            if phase - set(self['phase']):
-                print(f'Phase(s) {phase-set(self["phase"])} missing')
-                ok = False
-            if homogenization - set(self['homogenization']):
-                print(f'Homogenization(s) {homogenization-set(self["homogenization"])} missing')
-                ok = False
-
-        return ok
-
-
-    @property
-    def is_valid(self):
-        """Check for valid file layout."""
-        ok = True
-
-        if 'phase' in self:
-            for k,v in self['phase'].items():
-                if 'lattice' in v:
-                    try:
-                        Lattice(v['lattice'])
-                    except KeyError:
-                        s = v['lattice']
-                        print(f"Invalid lattice: '{s}' in phase '{k}'")
-                        ok = False
-
-        if 'microstructure' in self:
-            for i,v in enumerate(self['microstructure']):
-                if 'constituents' in v:
-                    f = 0.0
-                    for c in v['constituents']:
-                        f+= float(c['fraction'])
-                        if 'orientation' in c:
-                            try:
-                                Rotation.from_quaternion(c['orientation'])
-                            except ValueError:
-                                o = c['orientation']
-                                print(f"Invalid orientation: '{o}' in microstructure '{i}'")
-                                ok = False
-                    if not np.isclose(f,1.0):
-                        print(f"Invalid total fraction '{f}' in microstructure '{i}'")
-                        ok = False
-
-        return ok
-
-
-    def microstructure_rename_phase(self,mapping,ID=None,constituent=None):
-        """
-        Change phase name in microstructure.
-
-        Parameters
-        ----------
-        mapping: dictionary
-            Mapping from old name to new name
-        ID: list of ints, optional
-            Limit renaming to selected microstructure IDs.
-        constituent: list of ints, optional
-            Limit renaming to selected constituents.
-
-        """
-        dup = copy.deepcopy(self)
-        for i,m in enumerate(dup['microstructure']):
-            if ID and i not in ID: continue
-            for c in m['constituents']:
-                if constituent is not None and c not in constituent: continue
-                try:
-                    c['phase'] = mapping[c['phase']]
-                except KeyError:
-                    continue
-        return dup
-
-
-    def microstructure_rename_homogenization(self,mapping,ID=None):
-        """
-        Change homogenization name in microstructure.
-
-        Parameters
-        ----------
-        mapping: dictionary
-            Mapping from old name to new name
-        ID: list of ints, optional
-            Limit renaming to selected homogenization IDs.
-
-        """
-        dup = copy.deepcopy(self)
-        for i,m in enumerate(dup['microstructure']):
-            if ID and i not in ID: continue
-            try:
-                m['homogenization'] = mapping[m['homogenization']]
-            except KeyError:
-                continue
-        return dup

python/damask/_table.py

@@ -33,6 +33,10 @@ class Table:
         """Brief overview."""
         return util.srepr(self.comments)+'\n'+self.data.__repr__()
 
+    def __len__(self):
+        """Number of rows."""
+        return len(self.data)
+
     def __copy__(self):
         """Copy Table."""
         return copy.deepcopy(self)

python/tests/reference/ConfigMaterial/material.yaml

@@ -1,33 +1,35 @@
 homogenization:
   SX:
+    N_constituents: 2
     mech: {type: none}
   Taylor:
-    mech: {type: isostrain, N_constituents: 2}
+    N_constituents: 2
+    mech: {type: isostrain}
 
-microstructure:
+material:
   - constituents:
       - fraction: 1.0
-        orientation: [1.0, 0.0, 0.0, 0.0]
+        O: [1.0, 0.0, 0.0, 0.0]
         phase: Aluminum
     homogenization: SX
   - constituents:
       - fraction: 1.0
-        orientation: [0.7936696712125002, -0.28765777461664166, -0.3436487135089419, 0.4113964260949434]
+        O: [0.7936696712125002, -0.28765777461664166, -0.3436487135089419, 0.4113964260949434]
         phase: Aluminum
     homogenization: SX
   - constituents:
       - fraction: 1.0
-        orientation: [0.3986143167493579, -0.7014883552495493, 0.2154871765709027, 0.5500781677772945]
+        O: [0.3986143167493579, -0.7014883552495493, 0.2154871765709027, 0.5500781677772945]
         phase: Aluminum
     homogenization: SX
-  - homogenization: Taylor
+  - constituents:
-    constituents:
+      - fraction: 0.5
-      - fraction: .5
+        O: [0.28645844315788244, -0.022571491243423537, -0.467933059311115, -0.8357456192708106]
-        orientation: [0.28645844315788244, -0.022571491243423537, -0.467933059311115, -0.8357456192708106]
         phase: Aluminum
-      - fraction: .5
+      - fraction: 0.5
-        orientation: [0.3986143167493579, -0.7014883552495493, 0.2154871765709027, 0.5500781677772945]
+        O: [0.3986143167493579, -0.7014883552495493, 0.2154871765709027, 0.5500781677772945]
         phase: Steel
+    homogenization: Taylor
 
 phase:
   Aluminum:

python/tests/test_Config.py

@@ -0,0 +1,37 @@
+import pytest
+
+from damask import Config
+
+class TestConfig:
+
+    @pytest.mark.parametrize('flow_style',[None,True,False])
+    def test_load_save_str(self,tmp_path,flow_style):
+        config = Config()
+        config['A'] = 1
+        config['B'] = [2,3]
+        config.save(tmp_path/'config.yaml',default_flow_style=flow_style)
+        assert Config.load(tmp_path/'config.yaml') == config
+
+    def test_load_save_file(self,tmp_path):
+        config = Config()
+        config['A'] = 1
+        config['B'] = [2,3]
+        with open(tmp_path/'config.yaml','w') as f:
+            config.save(f)
+        with open(tmp_path/'config.yaml') as f:
+            assert Config.load(f) == config
+
+    def test_repr(self,tmp_path):
+        config = Config()
+        config['A'] = 1
+        config['B'] = [2,3]
+        with open(tmp_path/'config.yaml','w') as f:
+            f.write(config.__repr__())
+        assert Config.load(tmp_path/'config.yaml') == config
+
+
+    def test_abstract_is_valid(self):
+        assert Config().is_valid is None
+
+    def test_abstract_is_complete(self):
+        assert Config().is_complete is None

python/tests/test_ConfigMaterial.py

@@ -0,0 +1,76 @@
+import os
+
+import pytest
+
+from damask import ConfigMaterial
+
+@pytest.fixture
+def reference_dir(reference_dir_base):
+    """Directory containing reference results."""
+    return reference_dir_base/'ConfigMaterial'
+
+
+class TestConfigMaterial:
+
+    @pytest.mark.parametrize('fname',[None,'test.yaml'])
+    def test_load_save(self,reference_dir,tmp_path,fname):
+        reference = ConfigMaterial.load(reference_dir/'material.yaml')
+        os.chdir(tmp_path)
+        if fname is None:
+            reference.save()
+            new = ConfigMaterial.load('material.yaml')
+        else:
+            reference.save(fname)
+            new = ConfigMaterial.load(fname)
+        assert reference == new
+
+    def test_valid_complete(self,reference_dir):
+        material_config = ConfigMaterial.load(reference_dir/'material.yaml')
+        assert material_config.is_valid and material_config.is_complete
+
+    def test_invalid_lattice(self,reference_dir):
+        material_config = ConfigMaterial.load(reference_dir/'material.yaml')
+        material_config['phase']['Aluminum']['lattice']='fxc'
+        assert not material_config.is_valid
+
+    def test_invalid_orientation(self,reference_dir):
+        material_config = ConfigMaterial.load(reference_dir/'material.yaml')
+        material_config['material'][0]['constituents'][0]['O']=[0,0,0,0]
+        assert not material_config.is_valid
+
+    def test_invalid_fraction(self,reference_dir):
+        material_config = ConfigMaterial.load(reference_dir/'material.yaml')
+        material_config['material'][0]['constituents'][0]['fraction']=.9
+        assert not material_config.is_valid
+
+    @pytest.mark.parametrize('item',['homogenization','phase','material'])
+    def test_incomplete_missing(self,reference_dir,item):
+        material_config = ConfigMaterial.load(reference_dir/'material.yaml')
+        del material_config[item]
+        assert not material_config.is_complete
+
+    @pytest.mark.parametrize('item',['O','phase'])
+    def test_incomplete_material_constituent(self,reference_dir,item):
+        material_config = ConfigMaterial.load(reference_dir/'material.yaml')
+        del material_config['material'][0]['constituents'][0][item]
+        assert not material_config.is_complete
+
+    def test_incomplete_material_homogenization(self,reference_dir):
+        material_config = ConfigMaterial.load(reference_dir/'material.yaml')
+        del material_config['material'][0]['homogenization']
+        assert not material_config.is_complete
+
+    def test_incomplete_phase_lattice(self,reference_dir):
+        material_config = ConfigMaterial.load(reference_dir/'material.yaml')
+        del material_config['phase']['Aluminum']['lattice']
+        assert not material_config.is_complete
+
+    def test_incomplete_wrong_phase(self,reference_dir):
+        material_config = ConfigMaterial.load(reference_dir/'material.yaml')
+        new = material_config.material_rename_phase({'Steel':'FeNbC'})
+        assert not new.is_complete
+
+    def test_incomplete_wrong_homogenization(self,reference_dir):
+        material_config = ConfigMaterial.load(reference_dir/'material.yaml')
+        new = material_config.material_rename_homogenization({'Taylor':'isostrain'})
+        assert not new.is_complete

python/tests/test_Material.py

@@ -1,61 +0,0 @@
-import os
-
-import pytest
-
-from damask import Material
-
-@pytest.fixture
-def reference_dir(reference_dir_base):
-    """Directory containing reference results."""
-    return reference_dir_base/'Material'
-
-
-class TestMaterial:
-    
-    @pytest.mark.parametrize('fname',[None,'test.yaml'])
-    def test_load_save(self,reference_dir,tmp_path,fname):
-        reference = Material.load(reference_dir/'material.yaml')
-        os.chdir(tmp_path)
-        if fname is None:
-            reference.save()
-            new = Material.load('material.yaml')
-        else:
-            reference.save(fname)
-            new = Material.load(fname)
-        assert reference == new
-
-    def test_valid_complete(self,reference_dir):
-        material_config = Material.load(reference_dir/'material.yaml')
-        assert material_config.is_valid and material_config.is_complete
-
-    def test_invalid_lattice(self,reference_dir):
-        material_config = Material.load(reference_dir/'material.yaml')
-        material_config['phase']['Aluminum']['lattice']='fxc'
-        assert not material_config.is_valid
-    
-    def test_invalid_orientation(self,reference_dir):
-        material_config = Material.load(reference_dir/'material.yaml')
-        material_config['microstructure'][0]['constituents'][0]['orientation']=[0,0,0,0]
-        assert not material_config.is_valid
-    
-    def test_invalid_fraction(self,reference_dir):
-        material_config = Material.load(reference_dir/'material.yaml')
-        material_config['microstructure'][0]['constituents'][0]['fraction']=.9
-        assert not material_config.is_valid
-    
-
-    @pytest.mark.parametrize('item',['homogenization','phase','microstructure'])
-    def test_incomplete_missing(self,reference_dir,item):
-        material_config = Material.load(reference_dir/'material.yaml')
-        del material_config[item]
-        assert not material_config.is_complete
-    
-    def test_incomplete_wrong_phase(self,reference_dir):
-        material_config = Material.load(reference_dir/'material.yaml')
-        new = material_config.microstructure_rename_phase({'Steel':'FeNbC'})
-        assert not new.is_complete
-    
-    def test_incomplete_wrong_homogenization(self,reference_dir):
-        material_config = Material.load(reference_dir/'material.yaml')
-        new = material_config.microstructure_rename_homogenization({'Taylor':'isostrain'})
-        assert not new.is_complete

src/YAML_parse.f90

@@ -220,13 +220,26 @@ logical function isKey(line)
   if(len(IO_rmComment(line)) == 0) then
     isKey = .false.
   else
-    isKey = IO_rmComment(line(len(IO_rmComment(line)):len(IO_rmComment(line)))) == ':' &
+    isKey = index(IO_rmComment(line),':',back=.false.) == len(IO_rmComment(line)) .and. &
-                                                                .and. .not. isFlow(line)
+            index(IO_rmComment(line),':',back=.true.)  == len(IO_rmComment(line)) .and. &
+            .not. isFlow(line)
   endif
 
 end function isKey
 
 
+!--------------------------------------------------------------------------------------------------
+! @brief check whether a string is a list in flow style
+!--------------------------------------------------------------------------------------------------
+logical function isFlowList(line)
+
+  character(len=*), intent(in) :: line
+
+  isFlowList = index(adjustl(line),'[') == 1
+
+end function isFlowList
+
+
 !--------------------------------------------------------------------------------------------------
 ! @brief skip empty lines
 ! @details update start position in the block by skipping empty lines if present.
@@ -244,7 +257,6 @@ subroutine skip_empty_lines(blck,s_blck)
     if(empty) s_blck = s_blck + index(blck(s_blck:),IO_EOL)
   enddo
 
-
 end subroutine skip_empty_lines
  
 
@@ -273,6 +285,58 @@ subroutine skip_file_header(blck,s_blck)
 end subroutine skip_file_header
 
 
+!--------------------------------------------------------------------------------------------------
+!> @brief check if a line in flow YAML starts and ends in the same line
+!--------------------------------------------------------------------------------------------------
+logical function flow_is_closed(str,e_char)
+
+  character(len=*), intent(in) :: str
+  character,        intent(in) :: e_char                                                            !< end of list/dict  ( '}' or ']')
+  integer                      :: N_sq, &                                                           !< number of open square brackets
+                                  N_cu, &                                                           !< number of open curly brackets
+                                  i
+  character(len=:), allocatable:: line
+
+  flow_is_closed = .false.
+  N_sq = 0
+  N_cu = 0
+  if(e_char == ']') line = str(index(str(:),'[')+1:)
+  if(e_char == '}') line = str(index(str(:),'{')+1:)
+
+  do i = 1, len_trim(line)
+    flow_is_closed = (N_sq==0 .and. N_cu==0 .and. scan(line(i:i),e_char) == 1)
+    N_sq = N_sq + merge(1,0,line(i:i) == '[')
+    N_cu = N_cu + merge(1,0,line(i:i) == '{')
+    N_sq = N_sq - merge(1,0,line(i:i) == ']')
+    N_cu = N_cu - merge(1,0,line(i:i) == '}')
+  enddo
+
+end function flow_is_closed
+
+
+!--------------------------------------------------------------------------------------------------
+!> @brief return the flow YAML line without line break
+!--------------------------------------------------------------------------------------------------
+subroutine remove_line_break(blck,s_blck,e_char,flow_line)
+
+  character(len=*), intent(in)               :: blck                                                !< YAML in mixed style
+  integer,          intent(inout)            :: s_blck
+  character,        intent(in)               :: e_char                                              !< end of list/dict  ( '}' or ']')
+  character(len=:), allocatable, intent(out) :: flow_line
+  logical :: line_end
+
+  line_end =.false.
+  flow_line = ''
+
+  do while(.not.line_end)
+    flow_line = flow_line//IO_rmComment(blck(s_blck:s_blck + index(blck(s_blck:),IO_EOL) - 2))//' '
+    line_end  = flow_is_closed(flow_line,e_char)
+    s_blck    = s_blck + index(blck(s_blck:),IO_EOL)
+  enddo
+
+end subroutine remove_line_break
+
+
 !--------------------------------------------------------------------------------------------------
 ! @brief reads a line of YAML block which is already in flow style
 ! @details Dicts should be enlcosed within '{}' for it to be consistent with DAMASK YAML parser
@@ -402,7 +466,7 @@ recursive subroutine lst(blck,flow,s_blck,s_flow,offset)
   integer,          intent(inout) :: s_blck, &                                                      !< start position in blck
                                      s_flow, &                                                      !< start position in flow
                                      offset                                                         !< stores leading '- ' in nested lists
-  character(len=:), allocatable :: line
+  character(len=:), allocatable :: line,flow_line
   integer :: e_blck,indent
 
   indent = indentDepth(blck(s_blck:),offset)
@@ -437,8 +501,12 @@ recursive subroutine lst(blck,flow,s_blck,s_flow,offset)
           s_blck = e_blck +2
           offset = 0
         elseif(isFlow(line)) then
-          call line_isFlow(flow,s_flow,line)
+          if(isFlowList(line)) then
-          s_blck = e_blck +2
+            call remove_line_break(blck,s_blck,']',flow_line)
+          else
+            call remove_line_break(blck,s_blck,'}',flow_line)
+          endif
+          call line_isFlow(flow,s_flow,flow_line)
           offset = 0
         endif
       else                                                                                          ! list item in the same line
@@ -448,8 +516,13 @@ recursive subroutine lst(blck,flow,s_blck,s_flow,offset)
           s_blck = e_blck +2
           offset = 0
         elseif(isFlow(line)) then
-          call line_isFlow(flow,s_flow,line)
+          s_blck = s_blck + index(blck(s_blck:),'-')
-          s_blck = e_blck +2
+          if(isFlowList(line)) then
+            call remove_line_break(blck,s_blck,']',flow_line)
+          else
+            call remove_line_break(blck,s_blck,'}',flow_line)
+          endif
+          call line_isFlow(flow,s_flow,flow_line)
           offset = 0
         else                                                                                        ! non scalar list item
           offset = offset + indentDepth(blck(s_blck:))+1                                            ! offset in spaces to be ignored
@@ -486,8 +559,8 @@ recursive subroutine dct(blck,flow,s_blck,s_flow,offset)
                                      s_flow, &                                                      !< start position in flow
                                      offset
 
-  character(len=:), allocatable :: line
+  character(len=:), allocatable :: line,flow_line
-  integer :: e_blck,indent
+  integer :: e_blck,indent,col_pos
   logical :: previous_isKey
 
   previous_isKey = .false.
@@ -521,12 +594,22 @@ recursive subroutine dct(blck,flow,s_blck,s_flow,offset)
       endif
 
       if(isKeyValue(line)) then
+        col_pos = index(line,':')
+        if(isFlow(line(col_pos+1:))) then
+          if(isFlowList(line(col_pos+1:))) then
+            call remove_line_break(blck,s_blck,']',flow_line)
+          else
+            call remove_line_break(blck,s_blck,'}',flow_line)
+          endif
+          call keyValue_toFlow(flow,s_flow,flow_line)
+        else
           call keyValue_toFlow(flow,s_flow,line)
+          s_blck = e_blck + 2
+        endif
       else
         call line_toFlow(flow,s_flow,line)
+        s_blck = e_blck + 2
       endif
-
-      s_blck = e_blck +2
     end if
 
     if(isScalar(line) .or. isKeyValue(line)) then
@@ -559,7 +642,7 @@ recursive subroutine decide(blck,flow,s_blck,s_flow,offset)
                                      s_flow, &                                                      !< start position in flow
                                      offset
   integer :: e_blck
-  character(len=:), allocatable :: line
+  character(len=:), allocatable :: line,flow_line
 
   if(s_blck <= len(blck)) then
     call skip_empty_lines(blck,s_blck)
@@ -583,8 +666,12 @@ recursive subroutine decide(blck,flow,s_blck,s_flow,offset)
       flow(s_flow:s_flow) = '}'
       s_flow = s_flow + 1
     elseif(isFlow(line)) then
+      if(isFlowList(line)) then
+        call remove_line_break(blck,s_blck,']',flow_line)
+      else
+        call remove_line_break(blck,s_blck,'}',flow_line)
+      endif
       call line_isFlow(flow,s_flow,line)
-      s_blck = e_blck +2
     else
       line = line(indentDepth(line)+1:)
       call line_toFlow(flow,s_flow,line)
@@ -723,6 +810,36 @@ subroutine selfTest
   if (.not. to_flow(flow_mixed_braces)  == flow) error stop 'to_flow'
   end block basic_flow
 
+  multi_line_flow1: block
+  character(len=*), parameter :: flow_multi = &
+    "%YAML 1.1"//IO_EOL//&
+    "---"//IO_EOL//&
+    "a: [b,"//IO_EOL//&
+    "c: "//IO_EOL//&
+    "d, e]"//IO_EOL
+
+  character(len=*), parameter :: flow = &
+    "{a: [b, {c: d}, e]}"
+  
+  if( .not. to_flow(flow_multi)        == flow) error stop 'to_flow'
+  end block multi_line_flow1
+
+  multi_line_flow2: block
+  character(len=*), parameter :: flow_multi = &
+    "%YAML 1.1"//IO_EOL//&
+    "---"//IO_EOL//&
+    "-"//IO_EOL//&
+    " a: {b:"//IO_EOL//&
+    "[c,"//IO_EOL//&
+    "d"//IO_EOL//&
+    "e, f]}"//IO_EOL
+ 
+  character(len=*), parameter :: flow = &
+    "[{a: {b: [c, d e, f]}}]"
+
+  if( .not. to_flow(flow_multi)        == flow) error stop 'to_flow'
+  end block multi_line_flow2
+
   basic_mixed: block
   character(len=*), parameter :: block_flow = &
     "%YAML 1.1"//IO_EOL//&

src/YAML_types.f90

@@ -952,6 +952,9 @@ function tNode_get_byKey_asIndex(self,key)  result(keyIndex)
     endif
   enddo
 
+  if(keyIndex == -1) call IO_error(140,ext_msg=key)
+
+ 
 end function tNode_get_byKey_asIndex
 
 

src/constitutive.f90

@@ -452,11 +452,11 @@ subroutine constitutive_init
   PhaseLoop2:do p = 1,phases%length
 !--------------------------------------------------------------------------------------------------
 ! partition and initialize state
-    plasticState(p)%partionedState0 = plasticState(p)%state0
+    plasticState(p)%partitionedState0 = plasticState(p)%state0
-    plasticState(p)%state           = plasticState(p)%partionedState0
+    plasticState(p)%state             = plasticState(p)%partitionedState0
     forall(s = 1:phase_Nsources(p))
-      sourceState(p)%p(s)%partionedState0 = sourceState(p)%p(s)%state0
+      sourceState(p)%p(s)%partitionedState0 = sourceState(p)%p(s)%state0
-      sourceState(p)%p(s)%state           = sourceState(p)%p(s)%partionedState0
+      sourceState(p)%p(s)%state             = sourceState(p)%p(s)%partitionedState0
     end forall
 
     constitutive_source_maxSizeDotState   = max(constitutive_source_maxSizeDotState, &
@@ -922,7 +922,7 @@ subroutine constitutive_allocateState(state, &
 
   allocate(state%atol           (sizeState),             source=0.0_pReal)
   allocate(state%state0         (sizeState,NipcMyPhase), source=0.0_pReal)
-  allocate(state%partionedState0(sizeState,NipcMyPhase), source=0.0_pReal)
+  allocate(state%partitionedState0(sizeState,NipcMyPhase), source=0.0_pReal)
   allocate(state%subState0      (sizeState,NipcMyPhase), source=0.0_pReal)
   allocate(state%state          (sizeState,NipcMyPhase), source=0.0_pReal)
 

src/crystallite.f90

@@ -44,30 +44,30 @@ module crystallite
     !
     crystallite_Fp, &                                                                               !< current plastic def grad (end of converged time step)
     crystallite_Fp0, &                                                                              !< plastic def grad at start of FE inc
-    crystallite_partionedFp0,&                                                                      !< plastic def grad at start of homog inc
+    crystallite_partitionedFp0,&                                                                    !< plastic def grad at start of homog inc
     crystallite_subFp0,&                                                                            !< plastic def grad at start of crystallite inc
     !
     crystallite_Fi, &                                                                               !< current intermediate def grad (end of converged time step)
     crystallite_Fi0, &                                                                              !< intermediate def grad at start of FE inc
-    crystallite_partionedFi0,&                                                                      !< intermediate def grad at start of homog inc
+    crystallite_partitionedFi0,&                                                                    !< intermediate def grad at start of homog inc
     crystallite_subFi0,&                                                                            !< intermediate def grad at start of crystallite inc
     !
     crystallite_Lp0, &                                                                              !< plastic velocitiy grad at start of FE inc
-    crystallite_partionedLp0, &                                                                     !< plastic velocity grad at start of homog inc
+    crystallite_partitionedLp0, &                                                                   !< plastic velocity grad at start of homog inc
     !
     crystallite_Li, &                                                                               !< current intermediate velocitiy grad (end of converged time step)
     crystallite_Li0, &                                                                              !< intermediate velocitiy grad at start of FE inc
-    crystallite_partionedLi0, &                                                                     !< intermediate velocity grad at start of homog inc
+    crystallite_partitionedLi0, &                                                                   !< intermediate velocity grad at start of homog inc
     !
     crystallite_S0, &                                                                               !< 2nd Piola-Kirchhoff stress vector at start of FE inc
-    crystallite_partionedS0                                                                         !< 2nd Piola-Kirchhoff stress vector at start of homog inc
+    crystallite_partitionedS0                                                                       !< 2nd Piola-Kirchhoff stress vector at start of homog inc
   real(pReal),               dimension(:,:,:,:,:),    allocatable, public, protected :: &
     crystallite_P, &                                                                                !< 1st Piola-Kirchhoff stress per grain
     crystallite_Lp, &                                                                               !< current plastic velocitiy grad (end of converged time step)
     crystallite_S, &                                                                                !< current 2nd Piola-Kirchhoff stress vector (end of converged time step)
-    crystallite_partionedF0                                                                         !< def grad at start of homog inc
+    crystallite_partitionedF0                                                                       !< def grad at start of homog inc
   real(pReal),               dimension(:,:,:,:,:),    allocatable, public :: &
-    crystallite_partionedF                                                                         !< def grad to be reached at end of homog inc
+    crystallite_partitionedF                                                                        !< def grad to be reached at end of homog inc
 
   logical,                    dimension(:,:,:),         allocatable, public :: &
     crystallite_requested                                                                           !< used by upper level (homogenization) to request crystallite calculation
@@ -166,20 +166,20 @@ subroutine crystallite_init
   iMax = discretization_nIP
   eMax = discretization_nElem
 
-  allocate(crystallite_partionedF(3,3,cMax,iMax,eMax),source=0.0_pReal)
+  allocate(crystallite_partitionedF(3,3,cMax,iMax,eMax),source=0.0_pReal)
 
   allocate(crystallite_S0, &
            crystallite_F0, crystallite_Fi0,crystallite_Fp0, &
                            crystallite_Li0,crystallite_Lp0, &
-           crystallite_partionedS0, &
+           crystallite_partitionedS0, &
-           crystallite_partionedF0,crystallite_partionedFp0,crystallite_partionedFi0, &
+           crystallite_partitionedF0,crystallite_partitionedFp0,crystallite_partitionedFi0, &
-                                   crystallite_partionedLp0,crystallite_partionedLi0, &
+                                   crystallite_partitionedLp0,crystallite_partitionedLi0, &
            crystallite_S,crystallite_P, &
            crystallite_Fe,crystallite_Fi,crystallite_Fp, &
                           crystallite_Li,crystallite_Lp, &
            crystallite_subF,crystallite_subF0, &
            crystallite_subFp0,crystallite_subFi0, &
-           source = crystallite_partionedF)
+           source = crystallite_partitionedF)
 
   allocate(crystallite_dt(cMax,iMax,eMax),source=0.0_pReal)
   allocate(crystallite_subdt,crystallite_subFrac,crystallite_subStep, &
@@ -269,10 +269,10 @@ subroutine crystallite_init
   !$OMP END PARALLEL DO
 
 
-  crystallite_partionedFp0 = crystallite_Fp0
+  crystallite_partitionedFp0 = crystallite_Fp0
-  crystallite_partionedFi0 = crystallite_Fi0
+  crystallite_partitionedFi0 = crystallite_Fi0
-  crystallite_partionedF0  = crystallite_F0
+  crystallite_partitionedF0  = crystallite_F0
-  crystallite_partionedF   = crystallite_F0
+  crystallite_partitionedF   = crystallite_F0
 
   call crystallite_orientations()
 
@@ -280,8 +280,8 @@ subroutine crystallite_init
   do e = FEsolving_execElem(1),FEsolving_execElem(2)
     do i = FEsolving_execIP(1),FEsolving_execIP(2)
       do c = 1,homogenization_Ngrains(material_homogenizationAt(e))
-        call constitutive_dependentState(crystallite_partionedF0(1:3,1:3,c,i,e), &
+        call constitutive_dependentState(crystallite_partitionedF0(1:3,1:3,c,i,e), &
-                                         crystallite_partionedFp0(1:3,1:3,c,i,e), &
+                                         crystallite_partitionedFp0(1:3,1:3,c,i,e), &
                                          c,i,e)                                                     ! update dependent state variables to be consistent with basic states
      enddo
     enddo
@@ -325,8 +325,8 @@ function crystallite_stress()
 
   todo = .false.
 
-  subLp0 = crystallite_partionedLp0
+  subLp0 = crystallite_partitionedLp0
-  subLi0 = crystallite_partionedLi0
+  subLi0 = crystallite_partitionedLi0
 
 
 
@@ -338,15 +338,15 @@ function crystallite_stress()
     do i = FEsolving_execIP(1),FEsolving_execIP(2); do c = 1,homogenization_Ngrains(material_homogenizationAt(e))
       homogenizationRequestsCalculation: if (crystallite_requested(c,i,e)) then
         plasticState    (material_phaseAt(c,e))%subState0(      :,material_phaseMemberAt(c,i,e)) = &
-        plasticState    (material_phaseAt(c,e))%partionedState0(:,material_phaseMemberAt(c,i,e))
+        plasticState    (material_phaseAt(c,e))%partitionedState0(:,material_phaseMemberAt(c,i,e))
 
         do s = 1, phase_Nsources(material_phaseAt(c,e))
           sourceState(material_phaseAt(c,e))%p(s)%subState0(      :,material_phaseMemberAt(c,i,e)) = &
-          sourceState(material_phaseAt(c,e))%p(s)%partionedState0(:,material_phaseMemberAt(c,i,e))
+          sourceState(material_phaseAt(c,e))%p(s)%partitionedState0(:,material_phaseMemberAt(c,i,e))
         enddo
-        crystallite_subFp0(1:3,1:3,c,i,e) = crystallite_partionedFp0(1:3,1:3,c,i,e)
+        crystallite_subFp0(1:3,1:3,c,i,e) = crystallite_partitionedFp0(1:3,1:3,c,i,e)
-        crystallite_subFi0(1:3,1:3,c,i,e) = crystallite_partionedFi0(1:3,1:3,c,i,e)
+        crystallite_subFi0(1:3,1:3,c,i,e) = crystallite_partitionedFi0(1:3,1:3,c,i,e)
-        crystallite_subF0(1:3,1:3,c,i,e)  = crystallite_partionedF0(1:3,1:3,c,i,e)
+        crystallite_subF0(1:3,1:3,c,i,e)  = crystallite_partitionedF0(1:3,1:3,c,i,e)
         crystallite_subFrac(c,i,e) = 0.0_pReal
         crystallite_subStep(c,i,e) = 1.0_pReal/num%subStepSizeCryst
         todo(c,i,e) = .true.
@@ -426,8 +426,8 @@ function crystallite_stress()
 !  prepare for integration
           if (todo(c,i,e)) then
             crystallite_subF(1:3,1:3,c,i,e) = crystallite_subF0(1:3,1:3,c,i,e) &
-                                            + crystallite_subStep(c,i,e) *( crystallite_partionedF (1:3,1:3,c,i,e) &
+                                            + crystallite_subStep(c,i,e) *( crystallite_partitionedF (1:3,1:3,c,i,e) &
-                                                                           -crystallite_partionedF0(1:3,1:3,c,i,e))
+                                                                           -crystallite_partitionedF0(1:3,1:3,c,i,e))
             crystallite_Fe(1:3,1:3,c,i,e) = matmul(matmul(crystallite_subF(1:3,1:3,c,i,e), &
                                                           math_inv33(crystallite_Fp(1:3,1:3,c,i,e))), &
                                                    math_inv33(crystallite_Fi(1:3,1:3,c,i,e)))
@@ -441,8 +441,6 @@ function crystallite_stress()
     enddo elementLooping3
     !$OMP END PARALLEL DO
 
-    call nonlocalConvergenceCheck
-
 !--------------------------------------------------------------------------------------------------
 !  integrate --- requires fully defined state array (basic + dependent state)
     where(.not. crystallite_converged .and. crystallite_subStep > num%subStepMinCryst) &            ! do not try non-converged but fully cutbacked any further
@@ -475,17 +473,17 @@ subroutine crystallite_initializeRestorationPoints(i,e)
     s
 
   do c = 1,homogenization_Ngrains(material_homogenizationAt(e))
-    crystallite_partionedFp0(1:3,1:3,c,i,e) = crystallite_Fp0(1:3,1:3,c,i,e)
+    crystallite_partitionedFp0(1:3,1:3,c,i,e) = crystallite_Fp0(1:3,1:3,c,i,e)
-    crystallite_partionedLp0(1:3,1:3,c,i,e) = crystallite_Lp0(1:3,1:3,c,i,e)
+    crystallite_partitionedLp0(1:3,1:3,c,i,e) = crystallite_Lp0(1:3,1:3,c,i,e)
-    crystallite_partionedFi0(1:3,1:3,c,i,e) = crystallite_Fi0(1:3,1:3,c,i,e)
+    crystallite_partitionedFi0(1:3,1:3,c,i,e) = crystallite_Fi0(1:3,1:3,c,i,e)
-    crystallite_partionedLi0(1:3,1:3,c,i,e) = crystallite_Li0(1:3,1:3,c,i,e)
+    crystallite_partitionedLi0(1:3,1:3,c,i,e) = crystallite_Li0(1:3,1:3,c,i,e)
-    crystallite_partionedF0(1:3,1:3,c,i,e)  = crystallite_F0(1:3,1:3,c,i,e)
+    crystallite_partitionedF0(1:3,1:3,c,i,e)  = crystallite_F0(1:3,1:3,c,i,e)
-    crystallite_partionedS0(1:3,1:3,c,i,e)  = crystallite_S0(1:3,1:3,c,i,e)
+    crystallite_partitionedS0(1:3,1:3,c,i,e)  = crystallite_S0(1:3,1:3,c,i,e)
 
-    plasticState(material_phaseAt(c,e))%partionedState0(:,material_phasememberAt(c,i,e)) = &
+    plasticState(material_phaseAt(c,e))%partitionedState0(:,material_phasememberAt(c,i,e)) = &
     plasticState(material_phaseAt(c,e))%state0(         :,material_phasememberAt(c,i,e))
     do s = 1, phase_Nsources(material_phaseAt(c,e))
-      sourceState(material_phaseAt(c,e))%p(s)%partionedState0(:,material_phasememberAt(c,i,e)) = &
+      sourceState(material_phaseAt(c,e))%p(s)%partitionedState0(:,material_phasememberAt(c,i,e)) = &
       sourceState(material_phaseAt(c,e))%p(s)%state0(         :,material_phasememberAt(c,i,e))
     enddo
   enddo
@@ -506,17 +504,17 @@ subroutine crystallite_windForward(i,e)
     s
 
   do c = 1,homogenization_Ngrains(material_homogenizationAt(e))
-    crystallite_partionedF0 (1:3,1:3,c,i,e) = crystallite_partionedF(1:3,1:3,c,i,e)
+    crystallite_partitionedF0 (1:3,1:3,c,i,e) = crystallite_partitionedF(1:3,1:3,c,i,e)
-    crystallite_partionedFp0(1:3,1:3,c,i,e) = crystallite_Fp        (1:3,1:3,c,i,e)
+    crystallite_partitionedFp0(1:3,1:3,c,i,e) = crystallite_Fp        (1:3,1:3,c,i,e)
-    crystallite_partionedLp0(1:3,1:3,c,i,e) = crystallite_Lp        (1:3,1:3,c,i,e)
+    crystallite_partitionedLp0(1:3,1:3,c,i,e) = crystallite_Lp        (1:3,1:3,c,i,e)
-    crystallite_partionedFi0(1:3,1:3,c,i,e) = crystallite_Fi        (1:3,1:3,c,i,e)
+    crystallite_partitionedFi0(1:3,1:3,c,i,e) = crystallite_Fi        (1:3,1:3,c,i,e)
-    crystallite_partionedLi0(1:3,1:3,c,i,e) = crystallite_Li        (1:3,1:3,c,i,e)
+    crystallite_partitionedLi0(1:3,1:3,c,i,e) = crystallite_Li        (1:3,1:3,c,i,e)
-    crystallite_partionedS0 (1:3,1:3,c,i,e) = crystallite_S         (1:3,1:3,c,i,e)
+    crystallite_partitionedS0 (1:3,1:3,c,i,e) = crystallite_S         (1:3,1:3,c,i,e)
 
-    plasticState    (material_phaseAt(c,e))%partionedState0(:,material_phasememberAt(c,i,e)) = &
+    plasticState    (material_phaseAt(c,e))%partitionedState0(:,material_phasememberAt(c,i,e)) = &
     plasticState    (material_phaseAt(c,e))%state          (:,material_phasememberAt(c,i,e))
     do s = 1, phase_Nsources(material_phaseAt(c,e))
-      sourceState(material_phaseAt(c,e))%p(s)%partionedState0(:,material_phasememberAt(c,i,e)) = &
+      sourceState(material_phaseAt(c,e))%p(s)%partitionedState0(:,material_phasememberAt(c,i,e)) = &
       sourceState(material_phaseAt(c,e))%p(s)%state          (:,material_phasememberAt(c,i,e))
     enddo
   enddo
@@ -540,18 +538,18 @@ subroutine crystallite_restore(i,e,includeL)
 
   do c = 1,homogenization_Ngrains(material_homogenizationAt(e))
     if (includeL) then
-      crystallite_Lp(1:3,1:3,c,i,e) = crystallite_partionedLp0(1:3,1:3,c,i,e)
+      crystallite_Lp(1:3,1:3,c,i,e) = crystallite_partitionedLp0(1:3,1:3,c,i,e)
-      crystallite_Li(1:3,1:3,c,i,e) = crystallite_partionedLi0(1:3,1:3,c,i,e)
+      crystallite_Li(1:3,1:3,c,i,e) = crystallite_partitionedLi0(1:3,1:3,c,i,e)
     endif                                                                                           ! maybe protecting everything from overwriting makes more sense
-    crystallite_Fp(1:3,1:3,c,i,e)   = crystallite_partionedFp0(1:3,1:3,c,i,e)
+    crystallite_Fp(1:3,1:3,c,i,e)   = crystallite_partitionedFp0(1:3,1:3,c,i,e)
-    crystallite_Fi(1:3,1:3,c,i,e)   = crystallite_partionedFi0(1:3,1:3,c,i,e)
+    crystallite_Fi(1:3,1:3,c,i,e)   = crystallite_partitionedFi0(1:3,1:3,c,i,e)
-    crystallite_S (1:3,1:3,c,i,e)   = crystallite_partionedS0 (1:3,1:3,c,i,e)
+    crystallite_S (1:3,1:3,c,i,e)   = crystallite_partitionedS0 (1:3,1:3,c,i,e)
 
     plasticState    (material_phaseAt(c,e))%state(          :,material_phasememberAt(c,i,e)) = &
-    plasticState    (material_phaseAt(c,e))%partionedState0(:,material_phasememberAt(c,i,e))
+    plasticState    (material_phaseAt(c,e))%partitionedState0(:,material_phasememberAt(c,i,e))
     do s = 1, phase_Nsources(material_phaseAt(c,e))
       sourceState(material_phaseAt(c,e))%p(s)%state(          :,material_phasememberAt(c,i,e)) = &
-      sourceState(material_phaseAt(c,e))%p(s)%partionedState0(:,material_phasememberAt(c,i,e))
+      sourceState(material_phaseAt(c,e))%p(s)%partitionedState0(:,material_phasememberAt(c,i,e))
     enddo
   enddo
 
@@ -758,7 +756,7 @@ subroutine crystallite_results
     do o = 1, size(output_constituent(p)%label)
       select case (output_constituent(p)%label(o))
         case('F')
-          selected_tensors = select_tensors(crystallite_partionedF,p)
+          selected_tensors = select_tensors(crystallite_partitionedF,p)
           call results_writeDataset(group,selected_tensors,output_constituent(p)%label(o),&
                                    'deformation gradient','1')
         case('Fe')
@@ -943,7 +941,7 @@ function integrateStress(ipc,ip,el,timeFraction) result(broken)
     F  = crystallite_subF(1:3,1:3,ipc,ip,el)
   endif
 
-  call constitutive_dependentState(crystallite_partionedF(1:3,1:3,ipc,ip,el), &
+  call constitutive_dependentState(crystallite_partitionedF(1:3,1:3,ipc,ip,el), &
                                    crystallite_Fp(1:3,1:3,ipc,ip,el),ipc,ip,el)
 
   Lpguess = crystallite_Lp(1:3,1:3,ipc,ip,el)                                                       ! take as first guess
@@ -1120,9 +1118,9 @@ subroutine integrateStateFPI(g,i,e)
   c = material_phaseMemberAt(g,i,e)
 
   broken = constitutive_collectDotState(crystallite_S(1:3,1:3,g,i,e), &
-                                    crystallite_partionedF0, &
+                                    crystallite_partitionedF0, &
                                     crystallite_Fi(1:3,1:3,g,i,e), &
-                                    crystallite_partionedFp0, &
+                                    crystallite_partitionedFp0, &
                                     crystallite_subdt(g,i,e), g,i,e,p,c)
   if(broken) return
 
@@ -1152,9 +1150,9 @@ subroutine integrateStateFPI(g,i,e)
     if(broken) exit iteration
 
     broken = constitutive_collectDotState(crystallite_S(1:3,1:3,g,i,e), &
-                                          crystallite_partionedF0, &
+                                          crystallite_partitionedF0, &
                                           crystallite_Fi(1:3,1:3,g,i,e), &
-                                          crystallite_partionedFp0, &
+                                          crystallite_partitionedFp0, &
                                           crystallite_subdt(g,i,e), g,i,e,p,c)
     if(broken) exit iteration
 
@@ -1243,9 +1241,9 @@ subroutine integrateStateEuler(g,i,e)
   c = material_phaseMemberAt(g,i,e)
 
   broken = constitutive_collectDotState(crystallite_S(1:3,1:3,g,i,e), &
-                                    crystallite_partionedF0, &
+                                    crystallite_partitionedF0, &
                                     crystallite_Fi(1:3,1:3,g,i,e), &
-                                    crystallite_partionedFp0, &
+                                    crystallite_partitionedFp0, &
                                     crystallite_subdt(g,i,e), g,i,e,p,c)
   if(broken) return
 
@@ -1296,9 +1294,9 @@ subroutine integrateStateAdaptiveEuler(g,i,e)
   c = material_phaseMemberAt(g,i,e)
 
   broken = constitutive_collectDotState(crystallite_S(1:3,1:3,g,i,e), &
-                                        crystallite_partionedF0, &
+                                        crystallite_partitionedF0, &
                                         crystallite_Fi(1:3,1:3,g,i,e), &
-                                        crystallite_partionedFp0, &
+                                        crystallite_partitionedFp0, &
                                         crystallite_subdt(g,i,e), g,i,e,p,c)
   if(broken) return
 
@@ -1325,9 +1323,9 @@ subroutine integrateStateAdaptiveEuler(g,i,e)
   if(broken) return
 
   broken = constitutive_collectDotState(crystallite_S(1:3,1:3,g,i,e), &
-                                        crystallite_partionedF0, &
+                                        crystallite_partitionedF0, &
                                         crystallite_Fi(1:3,1:3,g,i,e), &
-                                        crystallite_partionedFp0, &
+                                        crystallite_partitionedFp0, &
                                         crystallite_subdt(g,i,e), g,i,e,p,c)
   if(broken) return
 
@@ -1434,9 +1432,9 @@ subroutine integrateStateRK(g,i,e,A,B,CC,DB)
   c = material_phaseMemberAt(g,i,e)
 
   broken = constitutive_collectDotState(crystallite_S(1:3,1:3,g,i,e), &
-                                        crystallite_partionedF0, &
+                                        crystallite_partitionedF0, &
                                         crystallite_Fi(1:3,1:3,g,i,e), &
-                                        crystallite_partionedFp0, &
+                                        crystallite_partitionedFp0, &
                                         crystallite_subdt(g,i,e), g,i,e,p,c)
   if(broken) return
 
@@ -1476,9 +1474,9 @@ subroutine integrateStateRK(g,i,e,A,B,CC,DB)
     if(broken) exit
 
     broken = constitutive_collectDotState(crystallite_S(1:3,1:3,g,i,e), &
-                                          crystallite_partionedF0, &
+                                          crystallite_partitionedF0, &
                                           crystallite_Fi(1:3,1:3,g,i,e), &
-                                          crystallite_partionedFp0, &
+                                          crystallite_partitionedFp0, &
                                           crystallite_subdt(g,i,e)*CC(stage), g,i,e,p,c)
     if(broken) exit
 
@@ -1526,38 +1524,6 @@ subroutine integrateStateRK(g,i,e,A,B,CC,DB)
 end subroutine integrateStateRK
 
 
-!--------------------------------------------------------------------------------------------------
-!> @brief sets convergence flag for nonlocal calculations
-!> @details one non-converged nonlocal sets all other nonlocals to non-converged to trigger cut back
-!--------------------------------------------------------------------------------------------------
-subroutine nonlocalConvergenceCheck
-
-  integer :: e,i,p
-  logical :: nonlocal_broken
-
-  nonlocal_broken = .false.
-  !$OMP PARALLEL DO PRIVATE(p)
-  do e = FEsolving_execElem(1),FEsolving_execElem(2)
-    p = material_phaseAt(1,e)
-    do i = FEsolving_execIP(1),FEsolving_execIP(2)
-      if(plasticState(p)%nonlocal .and. .not. crystallite_converged(1,i,e)) nonlocal_broken = .true.
-    enddo
-  enddo
-  !$OMP END PARALLEL DO
-
-  if(.not. nonlocal_broken) return
-  !$OMP PARALLEL DO PRIVATE(p)
-  do e = FEsolving_execElem(1),FEsolving_execElem(2)
-    p = material_phaseAt(1,e)
-    do i = FEsolving_execIP(1),FEsolving_execIP(2)
-      if(plasticState(p)%nonlocal) crystallite_converged(1,i,e) = .false.
-    enddo
-  enddo
-  !$OMP END PARALLEL DO
-
-end subroutine nonlocalConvergenceCheck
-
-
 !--------------------------------------------------------------------------------------------------
 !> @brief determines whether a point is converged
 !--------------------------------------------------------------------------------------------------
@@ -1590,7 +1556,7 @@ subroutine crystallite_restartWrite
   write(fileName,'(a,i0,a)') trim(getSolverJobName())//'_',worldrank,'.hdf5'
   fileHandle = HDF5_openFile(fileName,'a')
 
-  call HDF5_write(fileHandle,crystallite_partionedF,'F')
+  call HDF5_write(fileHandle,crystallite_partitionedF,'F')
   call HDF5_write(fileHandle,crystallite_Fp,        'Fp')
   call HDF5_write(fileHandle,crystallite_Fi,        'Fi')
   call HDF5_write(fileHandle,crystallite_Lp,        'Lp')
@@ -1665,7 +1631,7 @@ subroutine crystallite_forward
 
   integer :: i, j
 
-  crystallite_F0  = crystallite_partionedF
+  crystallite_F0  = crystallite_partitionedF
   crystallite_Fp0 = crystallite_Fp
   crystallite_Lp0 = crystallite_Lp
   crystallite_Fi0 = crystallite_Fi

src/homogenization.f90

@@ -404,16 +404,16 @@ subroutine partitionDeformation(subF,ip,el)
   chosenHomogenization: select case(homogenization_type(material_homogenizationAt(el)))
 
     case (HOMOGENIZATION_NONE_ID) chosenHomogenization
-      crystallite_partionedF(1:3,1:3,1,ip,el) = subF
+      crystallite_partitionedF(1:3,1:3,1,ip,el) = subF
 
     case (HOMOGENIZATION_ISOSTRAIN_ID) chosenHomogenization
       call mech_isostrain_partitionDeformation(&
-                           crystallite_partionedF(1:3,1:3,1:homogenization_Ngrains(material_homogenizationAt(el)),ip,el), &
+                           crystallite_partitionedF(1:3,1:3,1:homogenization_Ngrains(material_homogenizationAt(el)),ip,el), &
                            subF)
 
     case (HOMOGENIZATION_RGC_ID) chosenHomogenization
       call mech_RGC_partitionDeformation(&
-                          crystallite_partionedF(1:3,1:3,1:homogenization_Ngrains(material_homogenizationAt(el)),ip,el), &
+                          crystallite_partitionedF(1:3,1:3,1:homogenization_Ngrains(material_homogenizationAt(el)),ip,el), &
                           subF,&
                           ip, &
                           el)
@@ -448,8 +448,8 @@ function updateState(subdt,subF,ip,el)
       updateState = &
         updateState .and. &
           mech_RGC_updateState(crystallite_P(1:3,1:3,1:homogenization_Ngrains(material_homogenizationAt(el)),ip,el), &
-                               crystallite_partionedF(1:3,1:3,1:homogenization_Ngrains(material_homogenizationAt(el)),ip,el), &
+                               crystallite_partitionedF(1:3,1:3,1:homogenization_Ngrains(material_homogenizationAt(el)),ip,el), &
-                               crystallite_partionedF0(1:3,1:3,1:homogenization_Ngrains(material_homogenizationAt(el)),ip,el),&
+                               crystallite_partitionedF0(1:3,1:3,1:homogenization_Ngrains(material_homogenizationAt(el)),ip,el),&
                                subF,&
                                subdt, &
                                dPdFs, &

src/homogenization_mech_RGC.f90

@@ -212,7 +212,7 @@ end subroutine mech_RGC_init
 !--------------------------------------------------------------------------------------------------
 module subroutine mech_RGC_partitionDeformation(F,avgF,instance,of)
 
-  real(pReal),   dimension (:,:,:), intent(out) :: F                                                !< partioned F  per grain
+  real(pReal),   dimension (:,:,:), intent(out) :: F                                                !< partitioned F  per grain
 
   real(pReal),   dimension (3,3),   intent(in)  :: avgF                                             !< averaged F
   integer,                          intent(in)  :: &
@@ -867,7 +867,7 @@ module procedure mech_RGC_updateState
   !--------------------------------------------------------------------------------------------------
   subroutine grainDeformation(F, avgF, instance, of)
 
-    real(pReal),   dimension(:,:,:), intent(out) :: F                                               !< partioned F  per grain
+    real(pReal),   dimension(:,:,:), intent(out) :: F                                               !< partitioned F  per grain
 
     real(pReal),   dimension(:,:),   intent(in)  :: avgF                                            !< averaged F
     integer,                          intent(in)  :: &

src/prec.f90

@@ -47,7 +47,7 @@ module prec
       dotState, &                                                                                   !< rate of state change
       deltaState                                                                                    !< increment of state change
     real(pReal), allocatable, dimension(:,:) :: &
-      partionedState0, &
+      partitionedState0, &
       subState0
   end type
 

src/rotations.f90

@@ -737,13 +737,13 @@ pure function eu2om(eu) result(om)
   s = sin(eu)
 
   om(1,1) =  c(1)*c(3)-s(1)*s(3)*c(2)
-  om(1,2) =  s(1)*c(3)+c(1)*s(3)*c(2)
-  om(1,3) =  s(3)*s(2)
   om(2,1) = -c(1)*s(3)-s(1)*c(3)*c(2)
-  om(2,2) = -s(1)*s(3)+c(1)*c(3)*c(2)
-  om(2,3) =  c(3)*s(2)
   om(3,1) =  s(1)*s(2)
+  om(1,2) =  s(1)*c(3)+c(1)*s(3)*c(2)
+  om(2,2) = -s(1)*s(3)+c(1)*c(3)*c(2)
   om(3,2) = -c(1)*s(2)
+  om(1,3) =  s(3)*s(2)
+  om(2,3) =  c(3)*s(2)
   om(3,3) =  c(2)
 
   where(abs(om)<1.0e-12_pReal) om = 0.0_pReal