Merge branch 'new-ASCII' into grid-filters

.gitattributes

@@ -3,8 +3,8 @@
 # always use LF, even if the files are edited on windows, they need to be compiled/used on unix
 * text eol=lf
 
-installation/mods_Abaqus/abaqus_v6_windows.env eol=crlf 
 # Denote all files that are truly binary and should not be modified.
 *.png binary
 *.jpg binary
 *.cae binary
+*.hdf5 binary

.gitlab-ci.yml

@@ -1,6 +1,7 @@
 ---
 stages:
   - prepareAll
+  - python
   - preprocessing
   - postprocessing
   - compilePETSc
@@ -103,6 +104,16 @@ checkout:
     - master
     - release
 
+###################################################################################################
+Pytest:
+  stage: python
+  script:
+    - cd $DAMASKROOT/python
+    - pytest
+  except:
+    - master
+    - release
+
 ###################################################################################################
 OrientationRelationship:
   stage: preprocessing
@@ -308,13 +319,6 @@ nonlocal_densityConservation:
     - master
     - release
 
-Spectral_ipNeighborhood:
-  stage: grid
-  script: Spectral_ipNeighborhood/test.py
-  except:
-    - master
-    - release
-
 RGC_DetectChanges:
   stage: grid
   script: RGC_DetectChanges/test.py

PRIVATE

@@ -1 +1 @@
-Subproject commit a3a88933cbb92b81d481305ce93374917baf3980
+Subproject commit 66d562c755cd9aa4bbb8280c509383014acd52db

VERSION

@@ -1 +1 @@
-v2.0.3-1097-ga7fca4df
+v2.0.3-1133-gfede8225

examples/ConfigFiles/Crystallite_All.config

@@ -1,9 +0,0 @@
-[all]
-(output) orientation    # quaternion
-(output) grainrotation  # deviation from initial orientation as axis (1-3) and angle in degree (4) in crystal reference coordinates
-(output) F              # deformation gradient tensor
-(output) Fe             # elastic deformation gradient tensor
-(output) Fp             # plastic deformation gradient tensor
-(output) P              # first Piola-Kichhoff stress tensor
-(output) S              # second Piola-Kichhoff stress tensor
-(output) Lp             # plastic velocity gradient tensor

examples/SpectralMethod/Polycrystal/material.config

@@ -5,18 +5,6 @@
 [SX]
 mech	none
 
-#-------------------#
-<crystallite>
-#-------------------#
-[almostAll]
-(output) orientation    # quaternion
-(output) grainrotation  # deviation from initial orientation as axis (1-3) and angle in degree (4)
-(output) F              # deformation gradient tensor
-(output) Fe             # elastic deformation gradient tensor
-(output) Fp             # plastic deformation gradient tensor
-(output) P              # first Piola-Kichhoff stress tensor
-(output) Lp             # plastic velocity gradient tensor
-
 #-------------------#
 <phase>
 #-------------------#

processing/post/DADF5_postResults.py

@@ -59,14 +59,14 @@ for filename in options.filenames:
     data = np.concatenate((data,coords),1)
     header+=' 1_pos 2_pos 3_pos'
 
+    results.set_visible('materialpoints',False)
+    results.set_visible('constituents',  True)
     for label in options.con:
-      for p in results.iter_visible('con_physics'):
-        for c in results.iter_visible('constituents'):
       x = results.get_dataset_location(label)
       if len(x) == 0:
         continue
       array = results.read_dataset(x,0,plain=True)
-          d = int(np.product(np.shape(array)[1:]))
+      d = np.product(np.shape(array)[1:])
       data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
             
       if d>1:
@@ -74,14 +74,14 @@ for filename in options.filenames:
       else:
         header+=' '+label
 
+    results.set_visible('constituents',  False)
+    results.set_visible('materialpoints',True)
     for label in options.mat:
-      for p in results.iter_visible('mat_physics'):
-        for m in results.iter_visible('materialpoints'):
       x = results.get_dataset_location(label)
       if len(x) == 0:
         continue
       array = results.read_dataset(x,0,plain=True)
-          d = int(np.product(np.shape(array)[1:]))
+      d = np.product(np.shape(array)[1:])
       data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
           
       if d>1:

processing/post/DADF5_vtk_cells.py

@@ -74,7 +74,6 @@ for filename in options.filenames:
     results.set_visible('materialpoints',False)
     results.set_visible('constituents',  True)
     for label in options.con:
-      
       for p in results.iter_visible('con_physics'):
         if p != 'generic':
           for c in results.iter_visible('constituents'):

python/damask/table.py

@@ -29,6 +29,9 @@ class Table():
                 d[i] = label
                 i+=1
 
+        if i != self.data.shape[1]:
+            raise IndexError('Mismatch between array shape and headings')
+
         self.data.rename(columns=d,inplace=True)
 
         if comments is None:
@@ -44,8 +47,14 @@ class Table():
         Create table from ASCII file.
 
         The first line needs to indicate the number of subsequent header lines as 'n header'.
-        Vector data labels are indicated by '1_x, 2_x, ..., n_x'.
+        Vector data labels are indicated by '1_v, 2_v, ..., n_v'.
-        Tensor data labels are indicated by '3x3:1_x, 3x3:2_x, ..., 3x3:9_x'.
+        Tensor data labels are indicated by '3x3:1_T, 3x3:2_T, ..., 3x3:9_T'.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path
+            Filename or file for reading.
+
         """
         try:
             f = open(fname)
@@ -76,7 +85,15 @@ class Table():
         return Table(np.loadtxt(f),headings,comments)
 
     def get_array(self,label):
-        """Return data as array."""
+        """
+        Return data as array.
+
+        Parameters
+        ----------
+        label : str
+            Label of the array.
+
+        """
         if re.match(r'[0-9]*?_',label):
             idx,key = label.split('_',1)
             return self.data[key].to_numpy()[:,int(idx)-1]
@@ -84,7 +101,19 @@ class Table():
             return self.data[label].to_numpy().reshape((-1,)+self.headings[label])
 
     def set_array(self,label,array,info):
-        """Set data."""
+        """
+        Modify data in the spreadsheet.
+
+        Parameters
+        ----------
+        label : str
+            Label for the new data.
+        array : np.ndarray
+            New data.
+        info : str
+            Human-readable information about the new data.
+
+        """
         if np.prod(array.shape[1:],dtype=int) == 1: 
             self.comments.append('{}: {}'.format(label,info))
         else:
@@ -103,6 +132,19 @@ class Table():
         return [label for label in self.headings]
 
     def add_array(self,label,array,info):
+        """
+        Add data to the spreadsheet.
+
+        Parameters
+        ----------
+        label : str
+            Label for the new data.
+        array : np.ndarray
+            New data.
+        info : str
+            Human-readable information about the new data.
+
+        """
         if np.prod(array.shape[1:],dtype=int) == 1: 
             self.comments.append('{}: {}'.format(label,info))
         else:
@@ -115,6 +157,15 @@ class Table():
         self.data = pd.concat([self.data,new_data],axis=1)
         
     def to_ASCII(self,fname):
+        """
+        Store as plain text file.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path
+            Filename or file for reading.
+
+        """
         labels = []
         for l in self.headings:
             if(self.headings[l] == (1,)):
@@ -123,7 +174,7 @@ class Table():
                 labels+=['{}_{}'.format(i+1,l)\
                          for i in range(self.headings[l][0])]
             else:
-                labels+=['{}:{}_{}'.format(i+1,'x'.join([str(d) for d in self.headings[l]]),l)\
+                labels+=['{}:{}_{}'.format('x'.join([str(d) for d in self.headings[l]]),i+1,l)\
                                for i in range(np.prod(self.headings[l],dtype=int))]
 
         header = ['{} header'.format(len(self.comments)+1)]\

python/tests/conftest.py

@@ -0,0 +1,21 @@
+import os
+
+import pytest
+
+import damask
+
+def pytest_addoption(parser):
+    parser.addoption("--update",
+                     action="store_true",
+                     default=False)
+
+@pytest.fixture
+def update(request):
+    """Store current results as new reference results."""
+    return request.config.getoption("--update")
+
+@pytest.fixture
+def reference_dir_base():
+    """Directory containing reference results."""
+    env = damask.Environment()
+    return os.path.join(env.rootDir(),'python','tests','reference')

python/tests/reference/DADF5/12grains6x7x8.geom

@@ -0,0 +1,125 @@
+68 header
+geom_fromVoronoiTessellation 2.0.3-1073-g6f3cb071 
+<texture>
+[Grain1]
+(gauss)	phi1 358.98	Phi 65.62	phi2 24.48
+[Grain2]
+(gauss)	phi1 121.05	Phi 176.11	phi2 295.73
+[Grain3]
+(gauss)	phi1 43.79	Phi 113.76	phi2 345.90
+[Grain4]
+(gauss)	phi1 265.15	Phi 62.52	phi2 299.71
+[Grain5]
+(gauss)	phi1 221.23	Phi 26.54	phi2 207.05
+[Grain6]
+(gauss)	phi1 249.81	Phi 61.47	phi2 152.14
+[Grain7]
+(gauss)	phi1 332.45	Phi 99.16	phi2 345.34
+[Grain8]
+(gauss)	phi1 312.27	Phi 118.27	phi2 181.59
+[Grain9]
+(gauss)	phi1 303.10	Phi 48.21	phi2 358.03
+[Grain10]
+(gauss)	phi1 338.26	Phi 48.11	phi2 176.78
+[Grain11]
+(gauss)	phi1 115.17	Phi 56.54	phi2 223.84
+[Grain12]
+(gauss)	phi1 281.04	Phi 97.48	phi2 27.94
+<microstructure>
+[Grain1]
+crystallite 1
+(constituent)	phase 1	texture 1	fraction 1.0
+[Grain2]
+crystallite 1
+(constituent)	phase 1	texture 2	fraction 1.0
+[Grain3]
+crystallite 1
+(constituent)	phase 1	texture 3	fraction 1.0
+[Grain4]
+crystallite 1
+(constituent)	phase 1	texture 4	fraction 1.0
+[Grain5]
+crystallite 1
+(constituent)	phase 1	texture 5	fraction 1.0
+[Grain6]
+crystallite 1
+(constituent)	phase 1	texture 6	fraction 1.0
+[Grain7]
+crystallite 1
+(constituent)	phase 1	texture 7	fraction 1.0
+[Grain8]
+crystallite 1
+(constituent)	phase 1	texture 8	fraction 1.0
+[Grain9]
+crystallite 1
+(constituent)	phase 1	texture 9	fraction 1.0
+[Grain10]
+crystallite 1
+(constituent)	phase 1	texture 10	fraction 1.0
+[Grain11]
+crystallite 1
+(constituent)	phase 1	texture 11	fraction 1.0
+[Grain12]
+crystallite 1
+(constituent)	phase 1	texture 12	fraction 1.0
+<!skip>
+grid   a 6 b 7 c 8
+size   x 0.75 y 0.875 z 1.0
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
+ 9  3  3 10  9  9
+ 9  1  1  1  9  9
+ 9 11  1  1  7  9
+ 7 11 11  7  7  7
+ 7 11 11  7  7  7
+12  3  3 10  7 12
+12  3  3 10 10 12
+12  3  3  1  9  9
+ 9  1  1  1  9  9
+ 9  1  1  1  7  7
+ 7  1  1  7  7  7
+12 12  3  7  7  7
+12  3  3  3 12 12
+12  3  3  3 12 12
+12  3  3  1  1 12
+ 9  1  1  1  1  9
+ 6  1  1  1  8  8
+ 7  6  8  8  8  8
+12 12  8  8  8 12
+12  3  3  3 12 12
+12  3  3  3 12 12
+ 5  6  6  6  1 12
+ 6  6  6  6  8  8
+ 6  6  6  8  8  8
+ 8  6  8  8  8  8
+12  5  8  8  8  8
+12  5  5  8  8 12
+ 5  5  5  3 12 12
+ 5  5  6  6  6  5
+ 6  6  6  6  6  6
+ 6  6  6  6  8  8
+ 4  4  6  8  8  8
+ 4  4  2  2  2  8
+ 5  5  5  2  2  2
+ 5  5  5  5  2  5
+ 5  5  5 10 10  5
+ 6  6  6  6 10  4
+ 4  4 11 11  2  4
+ 4  4 11  2  2  4
+ 4  4  2  2  2  2
+ 5  5  5  2  2  2
+ 5  5  5 10 10  5
+ 5  5 10 10 10  9
+ 4 11 11 11 10  9
+ 4  4 11 11 11  4
+ 4  4 11 11  2  4
+ 4  4  2  2  2  2
+ 5  5  2  2  2  2
+ 5  5 10 10 10 10
+ 9 10 10 10 10  9
+ 9 11 11 10  9  9
+ 4 11 11 11  9  9
+ 4 11 11 11  7  7
+ 4  4 11  2  7  7
+12 10 10 10 10  7
+ 9 10 10 10 10  9

python/tests/reference/DADF5/material.config

@@ -0,0 +1,129 @@
+<homogenization>
+[none]
+mech none
+ngrains 1
+
+<texture>
+[Grain1]
+(gauss)	phi1 358.98	Phi 65.62	phi2 24.48
+[Grain2]
+(gauss)	phi1 121.05	Phi 176.11	phi2 295.73
+[Grain3]
+(gauss)	phi1 43.79	Phi 113.76	phi2 345.90
+[Grain4]
+(gauss)	phi1 265.15	Phi 62.52	phi2 299.71
+[Grain5]
+(gauss)	phi1 221.23	Phi 26.54	phi2 207.05
+[Grain6]
+(gauss)	phi1 249.81	Phi 61.47	phi2 152.14
+[Grain7]
+(gauss)	phi1 332.45	Phi 99.16	phi2 345.34
+[Grain8]
+(gauss)	phi1 312.27	Phi 118.27	phi2 181.59
+[Grain9]
+(gauss)	phi1 303.10	Phi 48.21	phi2 358.03
+[Grain10]
+(gauss)	phi1 338.26	Phi 48.11	phi2 176.78
+[Grain11]
+(gauss)	phi1 115.17	Phi 56.54	phi2 223.84
+[Grain12]
+(gauss)	phi1 281.04	Phi 97.48	phi2 27.94
+
+<microstructure>
+[Grain1]
+crystallite 1
+(constituent)	phase 1	texture 1	fraction 1.0
+[Grain2]
+crystallite 1
+(constituent)	phase 1	texture 2	fraction 1.0
+[Grain3]
+crystallite 1
+(constituent)	phase 1	texture 3	fraction 1.0
+[Grain4]
+crystallite 1
+(constituent)	phase 1	texture 4	fraction 1.0
+[Grain5]
+crystallite 1
+(constituent)	phase 1	texture 5	fraction 1.0
+[Grain6]
+crystallite 1
+(constituent)	phase 1	texture 6	fraction 1.0
+[Grain7]
+crystallite 1
+(constituent)	phase 2	texture 7	fraction 1.0
+[Grain8]
+crystallite 1
+(constituent)	phase 2	texture 8	fraction 1.0
+[Grain9]
+crystallite 1
+(constituent)	phase 2	texture 9	fraction 1.0
+[Grain10]
+crystallite 1
+(constituent)	phase 2	texture 10	fraction 1.0
+[Grain11]
+crystallite 1
+(constituent)	phase 2	texture 11	fraction 1.0
+[Grain12]
+crystallite 1
+(constituent)	phase 2	texture 12	fraction 1.0
+
+<phase>
+[pheno_fcc]
+elasticity              hooke
+plasticity              phenopowerlaw
+
+(output) orientation    # quaternion
+(output) F              # deformation gradient tensor
+(output) Fe             # elastic deformation gradient tensor
+(output) Fp             # plastic deformation gradient tensor
+(output) P              # first Piola-Kichhoff stress tensor
+(output) Lp             # plastic velocity gradient tensor
+
+
+lattice_structure       fcc
+Nslip                   12   # per family
+Ntwin                    0   # per family
+
+c11                     106.75e9
+c12                     60.41e9
+c44                     28.34e9
+
+gdot0_slip              0.001
+n_slip                  20
+tau0_slip                 31e6 # per family
+tausat_slip               63e6 # per family
+a_slip                  2.25
+h0_slipslip             75e6
+interaction_slipslip    1 1 1.4 1.4 1.4 1.4
+atol_resistance         1
+
+[pheno_bcc]
+elasticity              hooke
+plasticity              phenopowerlaw
+
+(output) orientation    # quaternion
+(output) F              # deformation gradient tensor
+(output) Fe             # elastic deformation gradient tensor
+(output) Fp             # plastic deformation gradient tensor
+(output) P              # first Piola-Kichhoff stress tensor
+(output) Lp             # plastic velocity gradient tensor
+
+
+lattice_structure       bcc
+Nslip                   12   # per family
+
+c11                     106.75e9
+c12                     60.41e9
+c44                     28.34e9
+
+gdot0_slip              0.001
+n_slip                  20
+tau0_slip                 31e6 # per family
+tausat_slip               63e6 # per family
+a_slip                  2.25
+h0_slipslip             75e6
+interaction_slipslip    1 1 1.4 1.4 1.4 1.4
+atol_resistance         1
+
+<crystallite>
+[dummy]

python/tests/reference/DADF5/tensionY.load

@@ -0,0 +1 @@
+fdot * 0 0 0 1.0e-3 0  0 0 *  stress  0 * *   * * *   * * 0  time 20  incs 40 freq 4

python/tests/reference/Geom/clean_stencil=1.geom

@@ -0,0 +1,25 @@
+4 header
+grid   a 8 b 5 c 4
+size   x 8e-06 y 5e-06 z 4e-06
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
+ 1  1  2 22  2  2  1 21
+ 1  1  6 26  2  2  5 25
+ 1  1 10 30  2  2  9 29
+ 1  1 14 34  2  2 13 33
+ 1  1 18 38  2  2 17 37
+ 1  1  3 23  2  2  2 22
+ 1  1  7 27  2  2  6 26
+ 1  1 11 31  2  2 10 30
+ 1  1 15 35  2  2 14 34
+ 1  1 19 39  2  2 18 38
+ 1  1  4 24  2  2  3 23
+ 1  1  8 28  2  2  7 27
+ 1  1 12 32  2  2 11 31
+ 1  1 16 36  2  2 15 35
+ 1  1 20 40  2  2 19 39
+ 1  1  5 25  2  2  4 24
+ 1  1  9 29  2  2  8 28
+ 1  1 13 33  2  2 12 32
+ 1  1 17 37  2  2 16 36
+ 1  1 21 41  2  2 20 40

python/tests/reference/Geom/clean_stencil=2.geom

@@ -0,0 +1,25 @@
+4 header
+grid   a 8 b 5 c 4
+size   x 8e-06 y 5e-06 z 4e-06
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
+ 1  1  1  2  2  2  1  1
+ 1  1  1  2  2  2  2  1
+ 1  1  1  6  2  2  2  5
+ 1  1  1 10  2  2  2  9
+ 1  1  1 14  2  2  2 13
+ 1  1  1  2  2  2  2  1
+ 1  1  1  2  2  2  2  1
+ 1  1  1  6  2  2  2  5
+ 1  1  1 10  2  2  2  9
+ 1  1  1 14  2  2  2 13
+ 1  1  1  3  2  2  2  2
+ 1  1  1  3  2  2  2  2
+ 1  1  1  7  2  2  2  6
+ 1  1  1 11  2  2  2 10
+ 1  1  1 15  2  2  2 14
+ 1  1  1  4  2  2  2  3
+ 1  1  1  4  2  2  2  3
+ 1  1  1  8  2  2  2  7
+ 1  1  1 12  2  2  2 11
+ 1  1  1 16  2  2  2 15

python/tests/reference/Geom/clean_stencil=3.geom

@@ -0,0 +1,25 @@
+4 header
+grid   a 8 b 5 c 4
+size   x 8e-06 y 5e-06 z 4e-06
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
+ 1  1  1  2  2  2  2 21
+ 1  1  1  2  2  2  2 21
+ 1  1  1  2  2  2  2 25
+ 1  1  1  2  2  2  2 29
+ 1  1  1  2  2  2  2 37
+ 1  1  1  2  2  2  2 21
+ 1  1  1  2  2  2  2 21
+ 1  1  1  2  2  2  2 25
+ 1  1  1  2  2  2  2 29
+ 1  1  1  2  2  2  2 37
+ 1  1  1  2  2  2  2 22
+ 1  1  1  2  2  2  2 22
+ 1  1  1  2  2  2  2 26
+ 1  1  1  2  2  2  2 30
+ 1  1  1  2  2  2  2 38
+ 1  1  1  2  2  2  2 24
+ 1  1  1  2  2  2  2 24
+ 1  1  1  2  2  2  2 28
+ 1  1  1  2  2  2  2 32
+ 1  1  1  2  2  2  2 40

python/tests/reference/Geom/clean_stencil=4.geom

@@ -0,0 +1,25 @@
+4 header
+grid   a 8 b 5 c 4
+size   x 8e-06 y 5e-06 z 4e-06
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
+1 1 1 2 2 2 2 2
+1 1 1 2 2 2 2 2
+1 1 1 2 2 2 2 2
+1 1 1 1 2 2 2 2
+1 1 1 1 2 2 2 2
+1 1 1 2 2 2 2 2
+1 1 1 2 2 2 2 2
+1 1 1 2 2 2 2 2
+1 1 1 1 2 2 2 2
+1 1 1 1 2 2 2 2
+1 1 1 2 2 2 2 2
+1 1 1 2 2 2 2 2
+1 1 1 2 2 2 2 2
+1 1 1 1 2 2 2 2
+1 1 1 1 2 2 2 2
+1 1 1 1 2 2 2 2
+1 1 1 1 2 2 2 2
+1 1 1 1 2 2 2 2
+1 1 1 1 2 2 2 2
+1 1 1 1 2 2 2 2

python/tests/reference/Geom/mirror_directions=x-y-z_reflect=True.geom

@@ -0,0 +1,85 @@
+4 header
+grid   a 16 b 10 c 8
+size   x 1.6e-05 y 1e-05 z 8e-06
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
+ 1  1  2 22  2  2  1 21 21  1  2  2 22  2  1  1
+ 1  1  6 26  2  2  5 25 25  5  2  2 26  6  1  1
+ 1  1 10 30  2  2  9 29 29  9  2  2 30 10  1  1
+ 1  1 14 34  2  2 13 33 33 13  2  2 34 14  1  1
+ 1  1 18 38  2  2 17 37 37 17  2  2 38 18  1  1
+ 1  1 18 38  2  2 17 37 37 17  2  2 38 18  1  1
+ 1  1 14 34  2  2 13 33 33 13  2  2 34 14  1  1
+ 1  1 10 30  2  2  9 29 29  9  2  2 30 10  1  1
+ 1  1  6 26  2  2  5 25 25  5  2  2 26  6  1  1
+ 1  1  2 22  2  2  1 21 21  1  2  2 22  2  1  1
+ 1  1  3 23  2  2  2 22 22  2  2  2 23  3  1  1
+ 1  1  7 27  2  2  6 26 26  6  2  2 27  7  1  1
+ 1  1 11 31  2  2 10 30 30 10  2  2 31 11  1  1
+ 1  1 15 35  2  2 14 34 34 14  2  2 35 15  1  1
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python/tests/reference/Geom/scale_grid=10-13-10.geom

@@ -0,0 +1,135 @@
+4 header
+grid   a 10 b 13 c 10
+size   x 8e-06 y 5e-06 z 4e-06
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
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python/tests/reference/Geom/scale_grid=10-20-2.geom

@@ -0,0 +1,45 @@
+4 header
+grid   a 10 b 20 c 2
+size   x 8e-06 y 5e-06 z 4e-06
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
+ 1  1  2  2 22  2  2  2  1 21
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+ 1  1 21 21 41  2  2  2 20 40

python/tests/reference/Geom/scale_grid=5-4-20.geom

@@ -0,0 +1,85 @@
+4 header
+grid   a 5 b 4 c 20
+size   x 8e-06 y 5e-06 z 4e-06
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
+ 1  2  2  2 21
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python/tests/reference/Geom/scale_grid=8-10-12.geom

@@ -0,0 +1,125 @@
+4 header
+grid   a 8 b 10 c 12
+size   x 8e-06 y 5e-06 z 4e-06
+origin x 0.0 y 0.0 z 0.0
+homogenization 1
+ 1  1  2 22  2  2  1 21
+ 1  1  2 22  2  2  1 21
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+ 1  1  6 26  2  2  5 25
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+ 1  1 14 34  2  2 13 33
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+ 1  1 18 38  2  2 17 37
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+ 1  1 10 30  2  2  9 29
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+ 1  1 14 34  2  2 13 33
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+ 1  1 18 38  2  2 17 37
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+ 1  1 12 32  2  2 11 31
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+ 1  1 20 40  2  2 19 39
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+ 1  1  4 24  2  2  3 23
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+ 1  1 12 32  2  2 11 31
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+ 1  1  5 25  2  2  4 24
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+ 1  1  9 29  2  2  8 28
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+ 1  1 17 37  2  2 16 36
+ 1  1 21 41  2  2 20 40
+ 1  1 21 41  2  2 20 40

python/tests/test_DADF5.py

@@ -0,0 +1,67 @@
+import shutil
+import os
+
+import pytest
+import numpy as np
+
+from damask import DADF5
+from damask import mechanics
+
+@pytest.fixture
+def default(tmp_path,reference_dir):
+    """Small DADF5 file in temp location for modification."""
+    fname = '12grains6x7x8_tensionY.hdf5'
+    shutil.copy(os.path.join(reference_dir,fname),tmp_path)
+    f = DADF5(os.path.join(tmp_path,fname))
+    f.set_by_time(20.0,20.0)
+    return f
+
+@pytest.fixture
+def reference_dir(reference_dir_base):
+    """Directory containing reference results."""
+    return os.path.join(reference_dir_base,'DADF5')
+
+
+class TestDADF5:
+    
+    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_Cauchy(self,default):
+        default.add_Cauchy('P','F')
+        loc = {'F':    default.get_dataset_location('F'),
+               'P':    default.get_dataset_location('P'),
+               'sigma':default.get_dataset_location('sigma')}
+        in_memory = mechanics.Cauchy(default.read_dataset(loc['F'],0),
+                                     default.read_dataset(loc['P'],0))
+        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'),
+               'det(P)': default.get_dataset_location('det(P)')}
+        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_spherical(self,default):
+        default.add_spherical('P')
+        loc = {'P':   default.get_dataset_location('P'),
+               'p_P': default.get_dataset_location('p_P')}
+        in_memory = mechanics.spherical_part(default.read_dataset(loc['P'],0)).reshape(-1,1)
+        in_file   = default.read_dataset(loc['p_P'],0)
+        assert np.allclose(in_memory,in_file)

python/tests/test_Geom.py

@@ -0,0 +1,99 @@
+import copy
+import os
+
+import pytest
+import numpy as np
+
+from damask import Geom
+
+
+def geom_equal(a,b):
+    return np.all(a.get_microstructure() == b.get_microstructure()) and \
+           np.all(a.get_size()           == b.get_size())           and \
+           np.all(a.get_grid()           == b.get_grid())
+
+@pytest.fixture
+def default():
+    """Simple geometry."""
+    x=np.concatenate((np.ones(40,dtype=int),
+                      np.arange(2,42),
+                      np.ones(40,dtype=int)*2,
+                      np.arange(1,41))).reshape((8,5,4))
+    return Geom(x,[8e-6,5e-6,4e-6])
+
+@pytest.fixture
+def reference_dir(reference_dir_base):
+    """Directory containing reference results."""
+    return os.path.join(reference_dir_base,'Geom')
+
+
+class TestGeom:
+    
+    def test_update(self,default):
+        modified = copy.deepcopy(default)
+        modified.update(
+                        default.get_microstructure(),
+                        default.get_size(),
+                        default.get_origin()
+                       )
+        assert geom_equal(modified,default)
+
+
+    def test_write_read_str(self,default,tmpdir):
+        default.to_file(str(tmpdir.join('default.geom')))
+        new = Geom.from_file(str(tmpdir.join('default.geom')))
+        assert geom_equal(new,default)
+
+    def test_write_read_file(self,default,tmpdir):
+        with open(tmpdir.join('default.geom'),'w') as f:
+            default.to_file(f)
+        with open(tmpdir.join('default.geom')) as f:
+            new = Geom.from_file(f)
+        assert geom_equal(new,default)
+
+    @pytest.mark.parametrize('pack',[True,False])
+    def test_pack(self,default,tmpdir,pack):
+        default.to_file(tmpdir.join('default.geom'),pack=pack)
+        new = Geom.from_file(tmpdir.join('default.geom'))
+        assert geom_equal(new,default)
+
+    @pytest.mark.parametrize('directions,reflect',[
+                                                   (['x'],        False),
+                                                   (['x','y','z'],True),
+                                                   (['z','x','y'],False),
+                                                   (['y','z'],    False)
+                                                  ]
+                            )
+    def test_mirror(self,default,update,reference_dir,directions,reflect):
+        modified = copy.deepcopy(default)
+        modified.mirror(directions,reflect)
+        tag = 'directions={}_reflect={}'.format('-'.join(directions),reflect)
+        reference = os.path.join(reference_dir,'mirror_{}.geom'.format(tag))
+        if update: modified.to_file(reference)
+        assert geom_equal(modified,Geom.from_file(reference))
+
+    @pytest.mark.parametrize('stencil',[(1),(2),(3),(4)])
+    def test_clean(self,default,update,reference_dir,stencil):
+        modified = copy.deepcopy(default)
+        modified.clean(stencil)
+        tag = 'stencil={}'.format(stencil)
+        reference = os.path.join(reference_dir,'clean_{}.geom'.format(tag))
+        if update: modified.to_file(reference)
+        assert geom_equal(modified,Geom.from_file(reference))
+
+    @pytest.mark.parametrize('grid',[
+                                     ((10,11,10)),
+                                     ([10,13,10]),
+                                     (np.array((10,10,10))),
+                                     (np.array((8, 10,12))),
+                                     (np.array((5, 4, 20))),
+                                     (np.array((10,20,2)) )
+                                    ]
+                            )
+    def test_scale(self,default,update,reference_dir,grid):
+        modified = copy.deepcopy(default)
+        modified.scale(grid)
+        tag = 'grid={}'.format('-'.join([str(x) for x in grid]))
+        reference = os.path.join(reference_dir,'scale_{}.geom'.format(tag))
+        if update: modified.to_file(reference)
+        assert geom_equal(modified,Geom.from_file(reference))

python/tests/test_Rotation.py

@@ -0,0 +1,55 @@
+import pytest
+import numpy as np
+
+from damask import Rotation
+   
+n = 1000
+
+@pytest.fixture
+def default():
+    """A set of n random rotations."""
+    return [Rotation.fromRandom() for r in range(n)]
+
+
+class TestRotation:
+
+    def test_Eulers(self,default):
+        for rot in default:
+            assert np.allclose(rot.asQuaternion(), 
+                               Rotation.fromEulers(rot.asEulers()).asQuaternion())
+
+
+    def test_AxisAngle(self,default):
+        for rot in default:
+            assert np.allclose(rot.asEulers(),
+                               Rotation.fromAxisAngle(rot.asAxisAngle()).asEulers())
+
+
+    def test_Matrix(self,default):
+        for rot in default:
+            assert np.allclose(rot.asAxisAngle(),
+                               Rotation.fromMatrix(rot.asMatrix()).asAxisAngle())
+
+
+    def test_Rodriques(self,default):
+        for rot in default:
+            assert np.allclose(rot.asMatrix(),
+                               Rotation.fromRodrigues(rot.asRodrigues()).asMatrix())
+
+
+    def test_Homochoric(self,default):
+        for rot in default:
+            assert np.allclose(rot.asRodrigues(),
+                               Rotation.fromHomochoric(rot.asHomochoric()).asRodrigues())
+
+
+    def test_Cubochoric(self,default):
+        for rot in default:
+            assert np.allclose(rot.asHomochoric(),
+                               Rotation.fromCubochoric(rot.asCubochoric()).asHomochoric())
+
+
+    def test_Quaternion(self,default):
+        for rot in default:
+            assert np.allclose(rot.asCubochoric(),
+                               Rotation.fromQuaternion(rot.asQuaternion()).asCubochoric())

python/tests/test_Table.py

@@ -0,0 +1,57 @@
+import pytest
+import numpy as np
+
+from damask import Table
+
+@pytest.fixture
+def default():
+    """Simple Table."""
+    x = np.ones((5,13))
+    return Table(x,{'F':(3,3),'v':(3,),'s':(1,)},['test data','contains only ones'])
+
+
+class TestTable:
+    
+    def test_get_tensor(self,default):
+        d = default.get_array('F')
+        assert np.allclose(d,1.0) and d.shape[1:] == (3,3) 
+
+    def test_get_vector(self,default):
+        d = default.get_array('v')
+        assert np.allclose(d,1.0) and d.shape[1:] == (3,)
+  
+    def test_write_read_str(self,default,tmpdir):
+        default.to_ASCII(str(tmpdir.join('default.txt')))
+        new = Table.from_ASCII(str(tmpdir.join('default.txt')))
+        assert all(default.data==new.data)
+
+    def test_write_read_file(self,default,tmpdir):
+        with open(tmpdir.join('default.txt'),'w') as f:
+            default.to_ASCII(f)
+        with open(tmpdir.join('default.txt')) as f:
+            new = Table.from_ASCII(f)
+        assert all(default.data==new.data)
+    
+    def test_set_array(self,default):
+        default.set_array('F',np.zeros((5,3,3)),'set to zero')
+        d=default.get_array('F')
+        assert np.allclose(d,0.0) and d.shape[1:] == (3,3)
+
+    def test_get_labels(self,default):
+        assert default.get_labels() == ['F','v','s']
+        
+    def test_add_array(self,default):
+        d = np.random.random((5,9))
+        default.add_array('nine',d,'random data')
+        assert np.allclose(d,default.get_array('nine'))
+
+
+    def test_invalid_initialization(self,default):
+        x = default.get_array('v')
+        with pytest.raises(IndexError):
+            Table(x,{'F':(3,3)})
+
+    def test_invalid_set(self,default):
+        x = default.get_array('v')
+        with pytest.raises(ValueError):
+            default.set_array('F',x,'does not work')

python/tests/test_mechanics.py

@@ -0,0 +1,142 @@
+import numpy as np
+from damask import mechanics
+
+class TestMechanics:
+   
+    n = 1000
+    c = np.random.randint(n)
+   
+
+    def test_vectorize_Cauchy(self):
+         P = np.random.random((self.n,3,3))
+         F = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.Cauchy(F,P)[self.c],
+                            mechanics.Cauchy(F[self.c],P[self.c]))
+
+
+    def test_vectorize_strain_tensor(self):
+         F = np.random.random((self.n,3,3))
+         t = ['V','U'][np.random.randint(0,2)]
+         m = np.random.random()*10. -5.0
+         assert np.allclose(mechanics.strain_tensor(F,t,m)[self.c],
+                            mechanics.strain_tensor(F[self.c],t,m))
+
+
+    def test_vectorize_deviatoric_part(self):
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.deviatoric_part(x)[self.c],
+                            mechanics.deviatoric_part(x[self.c]))
+
+
+    def test_vectorize_spherical_part(self):
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.spherical_part(x)[self.c],
+                            mechanics.spherical_part(x[self.c]))
+
+
+    def test_vectorize_Mises_stress(self):
+         sigma = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.Mises_stress(sigma)[self.c],
+                            mechanics.Mises_stress(sigma[self.c]))
+
+
+    def test_vectorize_Mises_strain(self):
+         epsilon = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.Mises_strain(epsilon)[self.c],
+                            mechanics.Mises_strain(epsilon[self.c]))
+
+
+    def test_vectorize_symmetric(self):
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.symmetric(x)[self.c],
+                            mechanics.symmetric(x[self.c]))
+
+
+    def test_vectorize_maximum_shear(self):
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.maximum_shear(x)[self.c],
+                            mechanics.maximum_shear(x[self.c]))
+
+
+    def test_vectorize_principal_components(self):
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.principal_components(x)[self.c],
+                            mechanics.principal_components(x[self.c]))
+
+
+    def test_vectorize_transpose(self):
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.transpose(x)[self.c],
+                            mechanics.transpose(x[self.c]))
+
+
+    def test_vectorize_rotational_part(self):
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.rotational_part(x)[self.c],
+                            mechanics.rotational_part(x[self.c]))
+
+
+    def test_vectorize_left_stretch(self):
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.left_stretch(x)[self.c],
+                            mechanics.left_stretch(x[self.c]))
+
+
+    def test_vectorize_right_stretch(self):
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.right_stretch(x)[self.c],
+                            mechanics.right_stretch(x[self.c]))
+
+
+    def test_Cauchy(self):
+         """Ensure Cauchy stress is symmetrized 1. Piola-Kirchhoff stress for no deformation."""
+         P = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.Cauchy(np.broadcast_to(np.eye(3),(self.n,3,3)),P),
+                            mechanics.symmetric(P))
+
+
+    def test_strain_tensor_no_rotation(self):
+         """Ensure that left and right stretch give same results for no rotation."""
+         F = np.broadcast_to(np.eye(3),[self.n,3,3])*np.random.random((self.n,3,3))
+         m = np.random.random()*20.0-10.0
+         assert np.allclose(mechanics.strain_tensor(F,'U',m),
+                            mechanics.strain_tensor(F,'V',m))
+   
+
+    def test_strain_tensor_rotation(self):
+         """Ensure that pure rotation results in no strain."""
+         F = mechanics.rotational_part(np.random.random((self.n,3,3)))
+         t = ['V','U'][np.random.randint(0,2)]
+         m = np.random.random()*2.0 - 1.0
+         assert np.allclose(mechanics.strain_tensor(F,t,m),
+                            0.0)
+   
+
+    def test_spherical_deviatoric_part(self):
+         """Ensure that full tensor is sum of spherical and deviatoric part."""
+         x = np.random.random((self.n,3,3))
+         sph = np.broadcast_to(np.eye(3),(self.n,3,3))\
+             * np.repeat(mechanics.spherical_part(x),9).reshape(self.n,3,3)
+         assert np.allclose(sph + mechanics.deviatoric_part(x),
+                            x)
+
+
+    def test_symmetric(self):
+         """Ensure that a symmetric tensor is half of the sum of a tensor and its transpose."""
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.symmetric(x)*2.0,
+                            mechanics.transpose(x)+x)
+
+
+    def test_transpose(self):
+         """Ensure that a symmetric tensor equals its transpose."""
+         x = mechanics.symmetric(np.random.random((self.n,3,3)))
+         assert np.allclose(mechanics.transpose(x),
+                            x)
+
+
+    def test_Mises(self):
+         """Ensure that equivalent stress is 3/2 of equivalent strain."""
+         x = np.random.random((self.n,3,3))
+         assert np.allclose(mechanics.Mises_stress(x)/mechanics.Mises_strain(x),
+                            1.5)

src/CPFEM2.f90

@@ -57,10 +57,10 @@ subroutine CPFEM_initAll
   call config_init
   call math_init
   call rotations_init
-  call mesh_init
   call lattice_init
   call HDF5_utilities_init
   call results_init
+  call mesh_init
   call material_init
   call constitutive_init
   call crystallite_init

src/config.f90

@@ -85,6 +85,7 @@ subroutine config_init
       case (trim('crystallite'))
         call parse_materialConfig(config_name_crystallite,config_crystallite,line,fileContent(i+1:))
         if (verbose) write(6,'(a)') ' Crystallite    parsed'; flush(6)
+        deallocate(config_crystallite)
     
       case (trim('homogenization'))
         call parse_materialConfig(config_name_homogenization,config_homogenization,line,fileContent(i+1:))
@@ -102,8 +103,6 @@ subroutine config_init
     call IO_error(160,ext_msg='<homogenization>')
   if (.not. allocated(config_microstructure) .or. size(config_microstructure) < 1) &
     call IO_error(160,ext_msg='<microstructure>')
-  if (.not. allocated(config_crystallite)    .or. size(config_crystallite)    < 1) &
-    call IO_error(160,ext_msg='<crystallite>')
   if (.not. allocated(config_phase)          .or. size(config_phase)          < 1) &
     call IO_error(160,ext_msg='<phase>')
   if (.not. allocated(config_texture)        .or. size(config_texture)        < 1) &
@@ -295,9 +294,6 @@ subroutine config_deallocate(what)
     case('material.config/microstructure')
       deallocate(config_microstructure)
 
-    case('material.config/crystallite')
-      deallocate(config_crystallite)
-
     case('material.config/homogenization')
       deallocate(config_homogenization)
 

src/crystallite.f90

@@ -22,22 +22,10 @@ module crystallite
   use discretization
   use lattice
   use plastic_nonlocal
-  use geometry_plastic_nonlocal, only: &
-    nIPneighbors    => geometry_plastic_nonlocal_nIPneighbors, &
-    IPneighborhood  => geometry_plastic_nonlocal_IPneighborhood
-  use HDF5_utilities
   use results
  
   implicit none 
   private
-  character(len=64),         dimension(:,:),          allocatable :: &
-    crystallite_output                                                                              !< name of each post result output
-  integer,                                                         public, protected :: &
-    crystallite_maxSizePostResults                                                                  !< description not available
-  integer,                   dimension(:),            allocatable, public, protected :: &
-    crystallite_sizePostResults                                                                     !< description not available
-  integer,                   dimension(:,:),          allocatable :: &
-    crystallite_sizePostResult                                                                      !< description not available
  
   real(pReal),               dimension(:,:,:),        allocatable, public :: &
     crystallite_dt                                                                                  !< requested time increment of each grain
@@ -90,21 +78,11 @@ module crystallite
  
   enum, bind(c)
     enumerator :: undefined_ID, &
-                  phase_ID, &
-                  texture_ID, &
                   orientation_ID, &
-                  grainrotation_ID, &
                   defgrad_ID, &
-                  fe_ID, &
                   fp_ID, &
-                  fi_ID, &
-                  lp_ID, &
-                  li_ID, &
                   p_ID, &
-                  s_ID, &
+                  elasmatrix_ID
-                  elasmatrix_ID, &
-                  neighboringip_ID, &
-                  neighboringelement_ID
   end enum
   integer(kind(undefined_ID)),dimension(:,:),   allocatable :: &
     crystallite_outputID                                                                            !< ID of each post result output
@@ -213,13 +191,6 @@ subroutine crystallite_init
   allocate(crystallite_requested(cMax,iMax,eMax),             source=.false.)
   allocate(crystallite_todo(cMax,iMax,eMax),                  source=.false.)
   allocate(crystallite_converged(cMax,iMax,eMax),             source=.true.)
-  allocate(crystallite_output(maxval(crystallite_Noutput), &
-                              size(config_crystallite))) ;       crystallite_output = ''
-  allocate(crystallite_outputID(maxval(crystallite_Noutput), &
-                              size(config_crystallite)),         source=undefined_ID)
-  allocate(crystallite_sizePostResults(size(config_crystallite)),source=0)
-  allocate(crystallite_sizePostResult(maxval(crystallite_Noutput), &
-                                      size(config_crystallite)), source=0)
                                       
   num%subStepMinCryst        = config_numerics%getFloat('substepmincryst',       defaultVal=1.0e-3_pReal)
   num%subStepSizeCryst       = config_numerics%getFloat('substepsizecryst',      defaultVal=0.25_pReal)
@@ -266,55 +237,6 @@ subroutine crystallite_init
       integrateState => integrateStateRKCK45
   end select
  
- 
- 
-  do c = 1, size(config_crystallite)
-#if defined(__GFORTRAN__)
-    str = ['GfortranBug86277']
-    str = config_crystallite(c)%getStrings('(output)',defaultVal=str)
-    if (str(1) == 'GfortranBug86277') str = [character(len=65536)::]
-#else
-    str = config_crystallite(c)%getStrings('(output)',defaultVal=[character(len=65536)::])
-#endif
-    do o = 1, size(str)
-      crystallite_output(o,c) = str(o)
-      outputName: select case(str(o))
-       case ('phase') outputName
-         crystallite_outputID(o,c) = phase_ID
-       case ('texture') outputName
-         crystallite_outputID(o,c) = texture_ID
-       case ('orientation') outputName
-         crystallite_outputID(o,c) = orientation_ID
-       case ('grainrotation') outputName
-         crystallite_outputID(o,c) = grainrotation_ID
-       case ('defgrad','f') outputName                                                              ! ToDo: no alias (f only)
-         crystallite_outputID(o,c) = defgrad_ID
-       case ('fe') outputName
-         crystallite_outputID(o,c) = fe_ID
-       case ('fp') outputName
-         crystallite_outputID(o,c) = fp_ID
-       case ('fi') outputName
-         crystallite_outputID(o,c) = fi_ID
-       case ('lp') outputName
-         crystallite_outputID(o,c) = lp_ID
-       case ('li') outputName
-         crystallite_outputID(o,c) = li_ID
-       case ('p','firstpiola','1stpiola') outputName                                                ! ToDo: no alias (p only)
-         crystallite_outputID(o,c) = p_ID
-       case ('s','tstar','secondpiola','2ndpiola') outputName                                       ! ToDo: no alias (s only)
-         crystallite_outputID(o,c) = s_ID
-       case ('elasmatrix') outputName
-         crystallite_outputID(o,c) = elasmatrix_ID
-       case ('neighboringip') outputName                                                            ! ToDo: this is not a result, it is static. Should be written out by mesh
-         crystallite_outputID(o,c) = neighboringip_ID
-       case ('neighboringelement') outputName                                                       ! ToDo: this is not a result, it is static. Should be written out by mesh
-         crystallite_outputID(o,c) = neighboringelement_ID
-       case default outputName
-         call IO_error(105,ext_msg=trim(str(o))//' (Crystallite)')
-      end select outputName
-    enddo
-  enddo
-  
   allocate(output_constituent(size(config_phase)))
   do c = 1, size(config_phase)
 #if defined(__GFORTRAN__)
@@ -327,47 +249,14 @@ subroutine crystallite_init
 #endif
   enddo
 
-
-  do r = 1,size(config_crystallite)
-    do o = 1,crystallite_Noutput(r)
-      select case(crystallite_outputID(o,r))
-        case(orientation_ID)
-          mySize = 4
-        case(defgrad_ID,fp_ID,p_ID)
-          mySize = 9
-        case(neighboringip_ID,neighboringelement_ID)
-          mySize = nIPneighbors
-        case default
-          mySize = 0
-      end select
-      crystallite_sizePostResult(o,r) = mySize
-      crystallite_sizePostResults(r) = crystallite_sizePostResults(r) + mySize
-    enddo
-  enddo
- 
-  crystallite_maxSizePostResults = &
-    maxval(crystallite_sizePostResults(microstructure_crystallite),microstructure_active)
- 
-
 !--------------------------------------------------------------------------------------------------
 ! write description file for crystallite output
   if (worldrank == 0) then
     call IO_write_jobFile(FILEUNIT,'outputCrystallite')
- 
+    write(FILEUNIT,'(/,a,/)') '[not supported anymore]'
-    do r = 1,size(config_crystallite)
-      if (any(microstructure_crystallite(discretization_microstructureAt) == r)) then
-        write(FILEUNIT,'(/,a,/)') '['//trim(config_name_crystallite(r))//']'
-        do o = 1,crystallite_Noutput(r)
-          write(FILEUNIT,'(a,i4)') trim(crystallite_output(o,r))//char(9),crystallite_sizePostResult(o,r)
-        enddo
-      endif
-    enddo
- 
     close(FILEUNIT)
   endif
- 
   call config_deallocate('material.config/phase')
-  call config_deallocate('material.config/crystallite')
 
 !--------------------------------------------------------------------------------------------------
 ! initialize
@@ -869,59 +758,21 @@ function crystallite_postResults(ipc, ip, el)
     ip, &                         !< integration point index
     ipc                           !< grain index
 
-  real(pReal), dimension(1+crystallite_sizePostResults(microstructure_crystallite(discretization_microstructureAt(el))) + &
+  real(pReal), dimension(1+ &
                          1+plasticState(material_phaseAt(ipc,el))%sizePostResults + &
                            sum(sourceState(material_phaseAt(ipc,el))%p(:)%sizePostResults)) :: &
     crystallite_postResults
   integer :: &
     o, &
     c, &
-    crystID, &
     mySize, &
     n
 
-  crystID = microstructure_crystallite(discretization_microstructureAt(el))
 
   crystallite_postResults = 0.0_pReal
-  crystallite_postResults(1) = real(crystallite_sizePostResults(crystID),pReal)                      ! header-like information (length)
+  crystallite_postResults(1) = 0.0_pReal                      ! header-like information (length)
   c = 1
 
-  do o = 1,crystallite_Noutput(crystID)
-    mySize = 0
-    select case(crystallite_outputID(o,crystID))
-      case (orientation_ID)
-        mySize = 4
-        crystallite_postResults(c+1:c+mySize) = crystallite_orientation(ipc,ip,el)%asQuaternion()
-
-! remark: tensor output is of the form 11,12,13, 21,22,23, 31,32,33
-! thus row index i is slow, while column index j is fast. reminder: "row is slow"
-
-      case (defgrad_ID)
-        mySize = 9
-        crystallite_postResults(c+1:c+mySize) = &
-          reshape(transpose(crystallite_partionedF(1:3,1:3,ipc,ip,el)),[mySize])
-      case (fp_ID)
-        mySize = 9
-        crystallite_postResults(c+1:c+mySize) = &
-          reshape(transpose(crystallite_Fp(1:3,1:3,ipc,ip,el)),[mySize])
-      case (p_ID)
-        mySize = 9
-        crystallite_postResults(c+1:c+mySize) = &
-          reshape(transpose(crystallite_P(1:3,1:3,ipc,ip,el)),[mySize])
-      case(neighboringelement_ID)
-        mySize = nIPneighbors
-        crystallite_postResults(c+1:c+mySize) = 0.0_pReal
-        forall (n = 1:mySize) &
-          crystallite_postResults(c+n) = real(IPneighborhood(1,n,ip,el),pReal)
-      case(neighboringip_ID)
-        mySize = nIPneighbors
-        crystallite_postResults(c+1:c+mySize) = 0.0_pReal
-        forall (n = 1:mySize) &
-          crystallite_postResults(c+n) = real(IPneighborhood(2,n,ip,el),pReal)
-    end select
-    c = c + mySize
-  enddo
-
   crystallite_postResults(c+1) = real(plasticState(material_phaseAt(ipc,el))%sizePostResults,pReal)  ! size of constitutive results
   c = c + 1
   if (size(crystallite_postResults)-c > 0) &
@@ -945,7 +796,7 @@ subroutine crystallite_results
   do p=1,size(config_name_phase)
     group = trim('current/constituent')//'/'//trim(config_name_phase(p))//'/generic'
     
-    call HDF5_closeGroup(results_addGroup(group))  
+    call results_closeGroup(results_addGroup(group))  
 
     do o = 1, size(output_constituent(p)%label)
       select case (output_constituent(p)%label(o))

src/discretization.f90

@@ -6,9 +6,6 @@ module discretization
 
   use prec
   use results
-#if defined(PETSc) || defined(DAMASK_HDF5)
-  use HDF5_utilities
-#endif
 
   implicit none
   private
@@ -84,7 +81,7 @@ subroutine discretization_results
 #if defined(PETSc) || defined(DAMASK_HDF5)
   real(pReal), dimension(:,:), allocatable :: u
   
-  call HDF5_closeGroup(results_addGroup(trim('current/geometry')))
+  call results_closeGroup(results_addGroup(trim('current/geometry')))
   
   u = discretization_NodeCoords (1:3,:discretization_sharedNodesBeginn) &
     - discretization_NodeCoords0(1:3,:discretization_sharedNodesBeginn)

src/geometry_plastic_nonlocal.f90

@@ -122,7 +122,7 @@ subroutine geometry_plastic_nonlocal_results
   
   integer,     dimension(:),   allocatable :: shp
 
-#if defined(DAMASK_HDF5)
+#if defined(PETSc) || defined(DAMASK_HDF5)
   call results_openJobFile
 
   writeVolume: block

src/grid/DAMASK_grid.f90

@@ -27,7 +27,6 @@ program DAMASK_spectral
  use grid_mech_FEM
  use grid_damage_spectral
  use grid_thermal_spectral
- use HDF5_utilities
  use results
  use rotations
 
@@ -319,15 +318,9 @@ program DAMASK_spectral
  enddo
  close(fileUnit)
 
- call results_openJobFile
- call HDF5_closeGroup(results_addGroup('geometry'))
- call results_addAttribute('grid',grid,'geometry')
- call results_addAttribute('size',geomSize,'geometry')
- call results_closeJobFile
-
 !--------------------------------------------------------------------------------------------------
 ! doing initialization depending on active solvers
- call Utilities_init()
+ call Utilities_init
  do field = 1, nActiveFields
    select case (loadCases(1)%ID(field))
      case(FIELD_MECH_ID)

src/homogenization.f90

@@ -262,7 +262,7 @@ subroutine homogenization_init
   materialpoint_sizeResults = 1 &                                                                   ! grain count
                             + 1 + thermal_maxSizePostResults        &
                                 + damage_maxSizePostResults         &
-                            + homogenization_maxNgrains * (1 + crystallite_maxSizePostResults &     ! crystallite size & crystallite results
+                            + homogenization_maxNgrains * (1 &     ! crystallite size
                                                          + 1 + constitutive_plasticity_maxSizePostResults & ! constitutive size & constitutive results
                                                              + constitutive_source_maxSizePostResults)
   allocate(materialpoint_results(materialpoint_sizeResults,discretization_nIP,discretization_nElem))
@@ -592,15 +592,13 @@ subroutine materialpoint_postResults
     thePos, &
     theSize, &
     myNgrains, &
-    myCrystallite, &
     g, &                                                                                            !< grain number
     i, &                                                                                            !< integration point number
     e                                                                                               !< element number
 
-  !$OMP PARALLEL DO PRIVATE(myNgrains,myCrystallite,thePos,theSize)
+  !$OMP PARALLEL DO PRIVATE(myNgrains,thePos,theSize)
   elementLooping: do e = FEsolving_execElem(1),FEsolving_execElem(2)
     myNgrains = homogenization_Ngrains(material_homogenizationAt(e))
-    myCrystallite = microstructure_crystallite(discretization_microstructureAt(e))
     IpLooping: do i = FEsolving_execIP(1,e),FEsolving_execIP(2,e)
       thePos = 0
 
@@ -618,7 +616,7 @@ subroutine materialpoint_postResults
       thePos = thePos + 1
 
       grainLooping :do g = 1,myNgrains
-        theSize = 1 + crystallite_sizePostResults(myCrystallite) + &
+        theSize = 1 + &
                   1 + plasticState    (material_phaseAt(g,e))%sizePostResults + &
                       sum(sourceState(material_phaseAt(g,e))%p(:)%sizePostResults)
         materialpoint_results(thePos+1:thePos+theSize,i,e) = crystallite_postResults(g,i,e)        ! tell crystallite results

src/material.f90

@@ -116,13 +116,11 @@ module material
     phase_Noutput, &                                                                                !< number of '(output)' items per phase
     phase_elasticityInstance, &                                                                     !< instance of particular elasticity of each phase
     phase_plasticityInstance, &                                                                     !< instance of particular plasticity of each phase
-    crystallite_Noutput, &                                                                          !< number of '(output)' items per crystallite setting
     homogenization_Ngrains, &                                                                       !< number of grains in each homogenization
     homogenization_Noutput, &                                                                       !< number of '(output)' items per homogenization
     homogenization_typeInstance, &                                                                  !< instance of particular type of each homogenization
     thermal_typeInstance, &                                                                         !< instance of particular type of each thermal transport
-    damage_typeInstance, &                                                                          !< instance of particular type of each nonlocal damage
+    damage_typeInstance                                                                             !< instance of particular type of each nonlocal damage
-    microstructure_crystallite                                                                      !< crystallite setting ID of each microstructure ! DEPRECATED !!!!
  
   real(pReal), dimension(:), allocatable, public, protected :: &
     thermal_initialT, &                                                                             !< initial temperature per each homogenization
@@ -245,9 +243,6 @@ subroutine material_init
   call material_parseMicrostructure()
   if (iand(myDebug,debug_levelBasic) /= 0) write(6,'(a)') ' Microstructure parsed'; flush(6)
   
-  call material_parseCrystallite()
-  if (iand(myDebug,debug_levelBasic) /= 0) write(6,'(a)') ' Crystallite    parsed'; flush(6)
-  
   call material_parseHomogenization()
   if (iand(myDebug,debug_levelBasic) /= 0) write(6,'(a)') ' Homogenization parsed'; flush(6)
   
@@ -277,9 +272,6 @@ subroutine material_init
   allocate(temperatureRate (material_Nhomogenization))
  
   do m = 1,size(config_microstructure)
-    if(microstructure_crystallite(m) < 1 .or. &
-       microstructure_crystallite(m) > size(config_crystallite)) &
-         call IO_error(150,m,ext_msg='crystallite')
     if(minval(microstructure_phase(1:microstructure_Nconstituents(m),m)) < 1 .or. &
        maxval(microstructure_phase(1:microstructure_Nconstituents(m),m)) > size(config_phase)) &
          call IO_error(150,m,ext_msg='phase')
@@ -298,8 +290,7 @@ subroutine material_init
     enddo
     write(6,'(/,a14,18x,1x,a11,1x,a12,1x,a13)') 'microstructure','crystallite','constituents'
     do m = 1,size(config_microstructure)
-      write(6,'(1x,a32,1x,i11,1x,i12)') config_name_microstructure(m), &
+      write(6,'(1x,a32,1x,i12)') config_name_microstructure(m), &
-                                        microstructure_crystallite(m), &
                                   microstructure_Nconstituents(m)
       if (microstructure_Nconstituents(m) > 0) then
         do c = 1,microstructure_Nconstituents(m)
@@ -500,7 +491,6 @@ subroutine material_parseMicrostructure
   character(len=65536) :: &
     tag
  
-  allocate(microstructure_crystallite(size(config_microstructure)),   source=0)
   allocate(microstructure_Nconstituents(size(config_microstructure)), source=0)
   allocate(microstructure_active(size(config_microstructure)),        source=.false.)
  
@@ -512,7 +502,6 @@ subroutine material_parseMicrostructure
  
   do m=1, size(config_microstructure)
     microstructure_Nconstituents(m) =  config_microstructure(m)%countKeys('(constituent)')
-    microstructure_crystallite(m)   =  config_microstructure(m)%getInt('crystallite')
   enddo
  
   microstructure_maxNconstituents = maxval(microstructure_Nconstituents)
@@ -547,21 +536,6 @@ subroutine material_parseMicrostructure
 end subroutine material_parseMicrostructure
 
 
-!--------------------------------------------------------------------------------------------------
-!> @brief parses the crystallite part in the material configuration file
-!--------------------------------------------------------------------------------------------------
-subroutine material_parseCrystallite
-
-  integer :: c
- 
-  allocate(crystallite_Noutput(size(config_crystallite)),source=0)
-  do c=1, size(config_crystallite)
-    crystallite_Noutput(c) = config_crystallite(c)%countKeys('(output)')
-  enddo
-
-end subroutine material_parseCrystallite
-
-
 !--------------------------------------------------------------------------------------------------
 !> @brief parses the phase part in the material configuration file
 !--------------------------------------------------------------------------------------------------

src/mesh_grid.f90

@@ -14,6 +14,7 @@ module mesh_grid
   use IO
   use debug
   use numerics
+  use results
   use discretization
   use geometry_plastic_nonlocal
   use FEsolving
@@ -99,6 +100,14 @@ subroutine mesh_init(ip,el)
   FEsolving_execElem = [1,product(myGrid)]                                                          ! parallel loop bounds set to comprise all elements
   allocate(FEsolving_execIP(2,product(myGrid)),source=1)                                            ! parallel loop bounds set to comprise the only IP
 
+!--------------------------------------------------------------------------------------------------
+! store geometry information for post processing
+  call results_openJobFile
+  call results_closeGroup(results_addGroup('geometry'))
+  call results_addAttribute('grid',grid,'geometry')
+  call results_addAttribute('size',geomSize,'geometry')
+  call results_closeJobFile
+
 !--------------------------------------------------------------------------------------------------
 ! geometry information required by the nonlocal CP model
   call geometry_plastic_nonlocal_setIPvolume(reshape([(product(mySize/real(myGrid,pReal)),j=1,product(myGrid))], &

src/mesh_marc.f90

@@ -119,15 +119,17 @@ subroutine mesh_init(ip,el)
                      reshape(connectivity_cell,[elem%NcellNodesPerCell,elem%nIPs*nElems]),&
                      node0_cell,ip_reshaped)
 
+!--------------------------------------------------------------------------------------------------
+! geometry information required by the nonlocal CP model
   call geometry_plastic_nonlocal_setIPvolume(IPvolume(elem,node0_cell,connectivity_cell))
   unscaledNormals = IPareaNormal(elem,nElems,connectivity_cell,node0_cell)
   call geometry_plastic_nonlocal_setIParea(norm2(unscaledNormals,1))
   call geometry_plastic_nonlocal_setIPareaNormal(unscaledNormals/spread(norm2(unscaledNormals,1),1,3))
   call geometry_plastic_nonlocal_results
   
-
 end subroutine mesh_init
 
+
 !--------------------------------------------------------------------------------------------------
 !> @brief Writes all information needed for the DADF5 geometry
 !--------------------------------------------------------------------------------------------------

src/results.f90

@@ -50,6 +50,7 @@ module results
     results_addIncrement, &
     results_addGroup, &
     results_openGroup, &
+    results_closeGroup, &
     results_writeDataset, &
     results_setLink, &
     results_addAttribute, &
@@ -120,6 +121,7 @@ subroutine results_addIncrement(inc,time)
 
 end subroutine results_addIncrement
 
+
 !--------------------------------------------------------------------------------------------------
 !> @brief open a group from the results file
 !--------------------------------------------------------------------------------------------------
@@ -144,6 +146,18 @@ integer(HID_T) function results_addGroup(groupName)
 end function results_addGroup
 
 
+!--------------------------------------------------------------------------------------------------
+!> @brief close a group
+!--------------------------------------------------------------------------------------------------
+subroutine results_closeGroup(group_id)
+
+  integer(HID_T), intent(in) :: group_id
+  
+  call HDF5_closeGroup(group_id)
+
+end subroutine results_closeGroup
+
+
 !--------------------------------------------------------------------------------------------------
 !> @brief set link to object in results file
 !--------------------------------------------------------------------------------------------------