Merge branch 'incs-no-leading-zero' into 'development'

Incs no leading zero

See merge request damask/DAMASK!108

processing/post/DADF5_postResults.py

@@ -47,6 +47,8 @@ for filename in options.filenames:
 
   coords = np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3) 
   
+  N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
+  N_digits = 5 # hack to keep test intact
   for i,inc in enumerate(results.iter_visible('increments')):
     print('Output step {}/{}'.format(i+1,len(results.increments)))
 
@@ -92,5 +94,6 @@ for filename in options.filenames:
     dirname  = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
     if not os.path.isdir(dirname):
       os.mkdir(dirname,0o755)
-    file_out = '{}_{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0],inc)
+    file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0],
+                                     inc[3:].zfill(N_digits))
     np.savetxt(os.path.join(dirname,file_out),data,header=header,comments='')

processing/post/DADF5_vtk_cells.py

@@ -66,7 +66,7 @@ for filename in options.filenames:
       for i in f['/geometry/T_c']:
         grid.InsertNextCell(vtk.VTK_HEXAHEDRON,8,i-1)
 
-
+  N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
   for i,inc in enumerate(results.iter_visible('increments')):
     print('Output step {}/{}'.format(i+1,len(results.increments)))
     vtk_data = []
@@ -132,7 +132,9 @@ for filename in options.filenames:
     dirname  = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
     if not os.path.isdir(dirname):
       os.mkdir(dirname,0o755)
-    file_out = '{}_{}.{}'.format(os.path.splitext(os.path.split(filename)[-1])[0],inc,writer.GetDefaultFileExtension())
+    file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.split(filename)[-1])[0],
+                                    inc[3:].zfill(N_digits),
+                                    writer.GetDefaultFileExtension())
     
     writer.SetCompressorTypeToZLib()
     writer.SetDataModeToBinary()

processing/post/DADF5_vtk_points.py

@@ -52,6 +52,7 @@ for filename in options.filenames:
   Polydata.SetVerts(Vertices)
   Polydata.Modified()
   
+  N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
   for i,inc in enumerate(results.iter_visible('increments')):
     print('Output step {}/{}'.format(i+1,len(results.increments)))
     vtk_data = []
@@ -111,7 +112,9 @@ for filename in options.filenames:
     dirname  = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
     if not os.path.isdir(dirname):
       os.mkdir(dirname,0o755)
-    file_out = '{}_{}.{}'.format(os.path.splitext(os.path.split(filename)[-1])[0],inc,writer.GetDefaultFileExtension())
+    file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.split(filename)[-1])[0],
+                                   inc[3:].zfill(N_digits),
+                                   writer.GetDefaultFileExtension())
     
     writer.SetCompressorTypeToZLib()
     writer.SetDataModeToBinary()

python/damask/dadf5.py

@@ -30,7 +30,14 @@ class DADF5():
     """
     with h5py.File(fname,'r') as f:
       
-      if f.attrs['DADF5-major'] != 0 or not 2 <= f.attrs['DADF5-minor'] <= 3:
+      try:
+        self.version_major = f.attrs['DADF5_version_major']
+        self.version_minor = f.attrs['DADF5_version_minor']
+      except KeyError:
+        self.version_major = f.attrs['DADF5-major']
+        self.version_minor = f.attrs['DADF5-minor']
+
+      if self.version_major != 0 or not 2 <= self.version_minor <= 4:
         raise TypeError('Unsupported DADF5 version {} '.format(f.attrs['DADF5-version']))
     
       self.structured = 'grid' in f['geometry'].attrs.keys()
@@ -40,8 +47,9 @@ class DADF5():
         self.size = f['geometry'].attrs['size']
         
       r=re.compile('inc[0-9]+')
-      self.increments = [i for i in f.keys() if r.match(i)]
+      increments_unsorted = {int(i[3:]):i for i in f.keys() if r.match(i)}
-      self.times      = [round(f[i].attrs['time/s'],12) for i in self.increments]
+      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.Nmaterialpoints, self.Nconstituents =   np.shape(f['mapping/cellResults/constituent'])
       self.materialpoints  = [m.decode() for m in np.unique(f['mapping/cellResults/materialpoint']['Name'])]
@@ -165,7 +173,10 @@ class DADF5():
       end increment (included)
 
     """
-    self.__manage_visible(['inc{:05d}'.format(i) for i in range(start,end+1)],'increments','set')
+    if self.version_minor >= 4:
+      self.__manage_visible([    'inc{}'.format(i) for i in range(start,end+1)],'increments','set')
+    else:
+      self.__manage_visible(['inc{:05d}'.format(i) for i in range(start,end+1)],'increments','set')
 
 
   def add_by_increment(self,start,end):
@@ -180,7 +191,10 @@ class DADF5():
       end increment (included)
 
     """
-    self.__manage_visible(['inc{:05d}'.format(i) for i in range(start,end+1)],'increments','add')
+    if self.version_minor >= 4:
+      self.__manage_visible([    'inc{}'.format(i) for i in range(start,end+1)],'increments','add')
+    else:
+      self.__manage_visible(['inc{:05d}'.format(i) for i in range(start,end+1)],'increments','add')
 
 
   def del_by_increment(self,start,end):
@@ -195,7 +209,10 @@ class DADF5():
       end increment (included)
 
     """
-    self.__manage_visible(['inc{:05d}'.format(i) for i in range(start,end+1)],'increments','del')
+    if self.version_minor >= 4:
+      self.__manage_visible([    'inc{}'.format(i) for i in range(start,end+1)],'increments','del')
+    else:
+      self.__manage_visible(['inc{:05d}'.format(i) for i in range(start,end+1)],'increments','del')
 
 
   def iter_visible(self,what):
@@ -420,6 +437,76 @@ class DADF5():
     else:
       with h5py.File(self.fname,'r') as f:
         return f['geometry/x_c'][()]
+    
+    
+  def add_absolute(self,x):
+    """
+    Add absolute value.
+
+    Parameters
+    ----------
+    x : str
+      Label of the dataset containing a scalar, vector, or tensor.
+
+    """
+    def __add_absolute(x):
+
+      return {
+              'data':  np.abs(x['data']),
+              'label': '|{}|'.format(x['label']),
+              'meta':  {
+                        'Unit':        x['meta']['Unit'],
+                        'Description': 'Absolute value of {} ({})'.format(x['label'],x['meta']['Description']),
+                        'Creator':     'dadf5.py:add_abs v{}'.format(version)
+                        }
+               }
+
+    requested = [{'label':x,'arg':'x'}]
+    
+    self.__add_generic_pointwise(__add_absolute,requested)
+    
+
+  def add_calculation(self,formula,label,unit='n/a',description=None,vectorized=True):
+    """
+    Add result of a general formula.
+    
+    Parameters
+    ----------
+    formula : str
+      Formula, refer to datasets by ‘#Label#‘.
+    label : str
+      Label of the dataset containing the result of the calculation.
+    unit : str, optional
+      Physical unit of the result.
+    description : str, optional
+      Human readable description of the result.
+    vectorized : bool, optional
+      Indicate whether the formula is written in vectorized form. Default is ‘True’.
+
+    """
+    if vectorized is not True:
+      raise NotImplementedError
+    
+    def __add_calculation(**kwargs):
+      
+      formula = kwargs['formula']
+      for d in re.findall(r'#(.*?)#',formula):
+        formula = formula.replace('#{}#'.format(d),"kwargs['{}']['data']".format(d))
+        
+      return {
+              'data':  eval(formula), 
+              'label': kwargs['label'],
+              'meta':  {
+                        'Unit':        kwargs['unit'],
+                        'Description': '{} (formula: {})'.format(kwargs['description'],kwargs['formula']),
+                        'Creator':     'dadf5.py:add_calculation v{}'.format(version)
+                        }
+               }
+    
+    requested    = [{'label':d,'arg':d} for d in set(re.findall(r'#(.*?)#',formula))]               # datasets used in the formula
+    pass_through = {'formula':formula,'label':label,'unit':unit,'description':description} 
+    
+    self.__add_generic_pointwise(__add_calculation,requested,pass_through)
 
 
   def add_Cauchy(self,P='P',F='F'):
@@ -453,6 +540,90 @@ class DADF5():
     self.__add_generic_pointwise(__add_Cauchy,requested)
 
 
+  def add_determinant(self,x):
+    """
+    Add the determinant of a tensor.
+
+    Parameters
+    ----------
+    x : str
+      Label of the dataset containing a tensor.
+
+    """
+    def __add_determinant(x):
+      
+      return {
+              'data':  np.linalg.det(x['data']),
+              'label': 'det({})'.format(x['label']),
+              'meta':  {
+                        'Unit':        x['meta']['Unit'],
+                        'Description': 'Determinant of tensor {} ({})'.format(x['label'],x['meta']['Description']),
+                        'Creator':     'dadf5.py:add_determinant v{}'.format(version)
+                        }
+              }
+      
+    requested = [{'label':x,'arg':'x'}]
+    
+    self.__add_generic_pointwise(__add_determinant,requested)
+
+
+  def add_deviator(self,x):
+    """
+    Add the deviatoric part of a tensor.
+
+    Parameters
+    ----------
+    x : str
+      Label of the dataset containing a tensor.
+
+    """
+    def __add_deviator(x):
+      
+      if not np.all(np.array(x['data'].shape[1:]) == np.array([3,3])):
+        raise ValueError
+      
+      return {
+              'data':  mechanics.deviatoric_part(x['data']),
+              'label': 's_{}'.format(x['label']),
+              'meta':  {
+                        'Unit':        x['meta']['Unit'],
+                        'Description': 'Deviator of tensor {} ({})'.format(x['label'],x['meta']['Description']),
+                        'Creator':     'dadf5.py:add_deviator v{}'.format(version)
+                        }
+               }
+      
+    requested = [{'label':x,'arg':'x'}]
+    
+    self.__add_generic_pointwise(__add_deviator,requested)
+    
+    
+  def add_maximum_shear(self,x):
+    """
+    Add maximum shear components of symmetric tensor.
+    
+    Parameters
+    ----------
+    x : str
+      Label of the dataset containing a symmetric tensor.
+
+    """
+    def __add_maximum_shear(x):
+
+      return {
+              'data':  mechanics.maximum_shear(x['data']),
+              'label': 'max_shear({})'.format(x['label']),
+              'meta':  {
+                        'Unit':        x['meta']['Unit'],
+                        'Description': 'Maximum shear component of of {} ({})'.format(x['label'],x['meta']['Description']),
+                        'Creator':     'dadf5.py:add_maximum_shear v{}'.format(version)
+                        }
+               }
+
+    requested = [{'label':x,'arg':'x'}]
+
+    self.__add_generic_pointwise(__add_maximum_shear,requested)
+
+
   def add_Mises(self,x):
     """
     Add the equivalent Mises stress or strain of a symmetric tensor.
@@ -523,58 +694,33 @@ class DADF5():
     self.__add_generic_pointwise(__add_norm,requested,{'ord':ord})
     
     
-  def add_absolute(self,x):
+  def add_principal_components(self,x):
     """
-    Add absolute value.
+    Add principal components of symmetric tensor.
-
+    
+    The principal components are sorted in descending order, each repeated according to its multiplicity.
+    
     Parameters
     ----------
     x : str
-      Label of the dataset containing a scalar, vector, or tensor.
+      Label of the dataset containing a symmetric tensor.
 
     """
-    def __add_absolute(x):
+    def __add_principal_components(x):
 
       return {
-              'data':  np.abs(x['data']),
+              'data':  mechanics.principal_components(x['data']),
-              'label': '|{}|'.format(x['label']),
+              'label': 'lambda_{}'.format(x['label']),
               'meta':  {
                         'Unit':        x['meta']['Unit'],
-                        'Description': 'Absolute value of {} ({})'.format(x['label'],x['meta']['Description']),
+                        'Description': 'Pricipal components of {} ({})'.format(x['label'],x['meta']['Description']),
-                        'Creator':     'dadf5.py:add_abs v{}'.format(version)
+                        'Creator':     'dadf5.py:add_principal_components v{}'.format(version)
                         }
                }
 
     requested = [{'label':x,'arg':'x'}]
-    
-    self.__add_generic_pointwise(__add_absolute,requested)
 
-
+    self.__add_generic_pointwise(__add_principal_components,requested)
-  def add_determinant(self,x):
-    """
-    Add the determinant of a tensor.
-
-    Parameters
-    ----------
-    x : str
-      Label of the dataset containing a tensor.
-
-    """
-    def __add_determinant(x):
-      
-      return {
-              'data':  np.linalg.det(x['data']),
-              'label': 'det({})'.format(x['label']),
-              'meta':  {
-                        'Unit':        x['meta']['Unit'],
-                        'Description': 'Determinant of tensor {} ({})'.format(x['label'],x['meta']['Description']),
-                        'Creator':     'dadf5.py:add_determinant v{}'.format(version)
-                        }
-              }
-      
-    requested = [{'label':x,'arg':'x'}]
-    
-    self.__add_generic_pointwise(__add_determinant,requested)
 
 
   def add_spherical(self,x):
@@ -607,79 +753,6 @@ class DADF5():
     self.__add_generic_pointwise(__add_spherical,requested)
 
 
-  def add_deviator(self,x):
-    """
-    Add the deviatoric part of a tensor.
-
-    Parameters
-    ----------
-    x : str
-      Label of the dataset containing a tensor.
-
-    """
-    def __add_deviator(x):
-      
-      if not np.all(np.array(x['data'].shape[1:]) == np.array([3,3])):
-        raise ValueError
-      
-      return {
-              'data':  mechanics.deviatoric_part(x['data']),
-              'label': 's_{}'.format(x['label']),
-              'meta':  {
-                        'Unit':        x['meta']['Unit'],
-                        'Description': 'Deviator of tensor {} ({})'.format(x['label'],x['meta']['Description']),
-                        'Creator':     'dadf5.py:add_deviator v{}'.format(version)
-                        }
-               }
-      
-    requested = [{'label':x,'arg':'x'}]
-    
-    self.__add_generic_pointwise(__add_deviator,requested)
-    
-
-  def add_calculation(self,formula,label,unit='n/a',description=None,vectorized=True):
-    """
-    Add result of a general formula.
-    
-    Parameters
-    ----------
-    formula : str
-      Formula, refer to datasets by ‘#Label#‘.
-    label : str
-      Label of the dataset containing the result of the calculation.
-    unit : str, optional
-      Physical unit of the result.
-    description : str, optional
-      Human readable description of the result.
-    vectorized : bool, optional
-      Indicate whether the formula is written in vectorized form. Default is ‘True’.
-
-    """
-    if vectorized is not True:
-      raise NotImplementedError
-    
-    def __add_calculation(**kwargs):
-      
-      formula = kwargs['formula']
-      for d in re.findall(r'#(.*?)#',formula):
-        formula = formula.replace('#{}#'.format(d),"kwargs['{}']['data']".format(d))
-        
-      return {
-              'data':  eval(formula), 
-              'label': kwargs['label'],
-              'meta':  {
-                        'Unit':        kwargs['unit'],
-                        'Description': '{} (formula: {})'.format(kwargs['description'],kwargs['formula']),
-                        'Creator':     'dadf5.py:add_calculation v{}'.format(version)
-                        }
-               }
-    
-    requested    = [{'label':d,'arg':d} for d in set(re.findall(r'#(.*?)#',formula))]               # datasets used in the formula
-    pass_through = {'formula':formula,'label':label,'unit':unit,'description':description} 
-    
-    self.__add_generic_pointwise(__add_calculation,requested,pass_through)
-
-
   def add_strain_tensor(self,F='F',t='U',m=0):
     """
     Add strain tensor calculated from a deformation gradient.
@@ -712,62 +785,6 @@ class DADF5():
     requested = [{'label':F,'arg':'F'}]
     
     self.__add_generic_pointwise(__add_strain_tensor,requested,{'t':t,'m':m})
-    
-    
-  def add_principal_components(self,x):
-    """
-    Add principal components of symmetric tensor.
-    
-    The principal components are sorted in descending order, each repeated according to its multiplicity.
-    
-    Parameters
-    ----------
-    x : str
-      Label of the dataset containing a symmetric tensor.
-
-    """
-    def __add_principal_components(x):
-
-      return {
-              'data':  mechanics.principal_components(x['data']),
-              'label': 'lambda_{}'.format(x['label']),
-              'meta':  {
-                        'Unit':        x['meta']['Unit'],
-                        'Description': 'Pricipal components of {} ({})'.format(x['label'],x['meta']['Description']),
-                        'Creator':     'dadf5.py:add_principal_components v{}'.format(version)
-                        }
-               }
-
-    requested = [{'label':x,'arg':'x'}]
-
-    self.__add_generic_pointwise(__add_principal_components,requested)
-    
-    
-  def add_maximum_shear(self,x):
-    """
-    Add maximum shear components of symmetric tensor.
-    
-    Parameters
-    ----------
-    x : str
-      Label of the dataset containing a symmetric tensor.
-
-    """
-    def __add_maximum_shear(x):
-
-      return {
-              'data':  mechanics.maximum_shear(x['data']),
-              'label': 'max_shear({})'.format(x['label']),
-              'meta':  {
-                        'Unit':        x['meta']['Unit'],
-                        'Description': 'Maximum shear component of of {} ({})'.format(x['label'],x['meta']['Description']),
-                        'Creator':     'dadf5.py:add_maximum_shear v{}'.format(version)
-                        }
-               }
-
-    requested = [{'label':x,'arg':'x'}]
-
-    self.__add_generic_pointwise(__add_maximum_shear,requested)
 
 
   def __add_generic_pointwise(self,func,datasets_requested,extra_args={}):

python/tests/test_DADF5.py

@@ -23,13 +23,20 @@ def reference_dir(reference_dir_base):
 
 
 class TestDADF5:
-    
+
-    def test_add_deviator(self,default):
+    def test_time_increments(self,default):
-        default.add_deviator('P')
+        shape = default.read_dataset(default.get_dataset_location('F'),0).shape
-        loc = {'P'  :default.get_dataset_location('P'),
+        default.set_by_time(0.0,20.0)
-               's_P':default.get_dataset_location('s_P')}
+        for i in default.iter_visible('increments'):
-        in_memory = mechanics.deviatoric_part(default.read_dataset(loc['P'],0))
+           assert shape == default.read_dataset(default.get_dataset_location('F'),0).shape
-        in_file   = default.read_dataset(loc['s_P'],0)
+
+
+    def test_add_absolute(self,default):
+        default.add_absolute('Fe')
+        loc = {'Fe':   default.get_dataset_location('Fe'),
+               '|Fe|': default.get_dataset_location('|Fe|')}
+        in_memory = np.abs(default.read_dataset(loc['Fe'],0))
+        in_file   = default.read_dataset(loc['|Fe|'],0)
         assert np.allclose(in_memory,in_file)
 
     def test_add_Cauchy(self,default):
@@ -42,22 +49,30 @@ class TestDADF5:
         in_file   = default.read_dataset(loc['sigma'],0)
         assert np.allclose(in_memory,in_file)
 
-    def test_add_absolute(self,default):
-        default.add_absolute('Fe')
-        loc = {'Fe':   default.get_dataset_location('Fe'),
-               '|Fe|': default.get_dataset_location('|Fe|')}
-        in_memory = np.abs(default.read_dataset(loc['Fe'],0))
-        in_file   = default.read_dataset(loc['|Fe|'],0)
-        assert np.allclose(in_memory,in_file)
-
     def test_add_determinant(self,default):
         default.add_determinant('P')
-        loc = {'P':      default.get_dataset_location('P'),
+        loc = {'P':     default.get_dataset_location('P'),
-               'det(P)': default.get_dataset_location('det(P)')}
+               'det(P)':default.get_dataset_location('det(P)')}
-        in_memory = np.linalg.det(default.read_dataset(loc['P'],0)).reshape(-1,1)
+        in_memory = np.linalg.det(default.read_dataset(loc['P'],0)).reshape((-1,1))
         in_file   = default.read_dataset(loc['det(P)'],0)
         assert np.allclose(in_memory,in_file)
 
+    def test_add_deviator(self,default):
+        default.add_deviator('P')
+        loc = {'P'  :default.get_dataset_location('P'),
+               's_P':default.get_dataset_location('s_P')}
+        in_memory = mechanics.deviatoric_part(default.read_dataset(loc['P'],0))
+        in_file   = default.read_dataset(loc['s_P'],0)
+        assert np.allclose(in_memory,in_file)
+
+    def test_add_norm(self,default):
+        default.add_norm('F',1)
+        loc = {'F':    default.get_dataset_location('F'),
+               '|F|_1':default.get_dataset_location('|F|_1')}
+        in_memory = np.linalg.norm(default.read_dataset(loc['F'],0),ord=1,axis=(1,2),keepdims=True)
+        in_file   = default.read_dataset(loc['|F|_1'],0)
+        assert np.allclose(in_memory,in_file)
+
     def test_add_spherical(self,default):
         default.add_spherical('P')
         loc = {'P':   default.get_dataset_location('P'),

src/results.f90

@@ -69,10 +69,9 @@ subroutine results_init
   write(6,'(a)')   ' https://doi.org/10.1007/s40192-017-0084-5'
 
   resultsFile = HDF5_openFile(trim(getSolverJobName())//'.hdf5','w',.true.)
-  call HDF5_addAttribute(resultsFile,'DADF5-version',0.3_pReal)
+  call HDF5_addAttribute(resultsFile,'DADF5_version_major',0)
-  call HDF5_addAttribute(resultsFile,'DADF5-major',0)
+  call HDF5_addAttribute(resultsFile,'DADF5_version_minor',4)
-  call HDF5_addAttribute(resultsFile,'DADF5-minor',3)
+  call HDF5_addAttribute(resultsFile,'DAMASK_version',DAMASKVERSION)
-  call HDF5_addAttribute(resultsFile,'DAMASK',DAMASKVERSION)
   call get_command(commandLine)
   call HDF5_addAttribute(resultsFile,'call',trim(commandLine))
   call HDF5_closeGroup(results_addGroup('mapping'))
@@ -111,7 +110,7 @@ subroutine results_addIncrement(inc,time)
   real(pReal),   intent(in) :: time
   character(len=pStringLen) :: incChar
 
-  write(incChar,'(i5.5)') inc                                                                       ! allow up to 99999 increments
+  write(incChar,'(i10)') inc
   call HDF5_closeGroup(results_addGroup(trim('inc'//trim(adjustl(incChar)))))
   call results_setLink(trim('inc'//trim(adjustl(incChar))),'current')
   call HDF5_addAttribute(resultsFile,'time/s',time,trim('inc'//trim(adjustl(incChar))))