Merge branch 'vtr-only' into development

.gitlab-ci.yml

@@ -285,20 +285,6 @@ grid_all_restart:
     - master
     - release
 
-grid_parsingLoadCase:
-  stage: grid
-  script: grid_parsingLoadCase/test.py
-  except:
-    - master
-    - release
-
-grid_all_loadCaseRotation:
-  stage: grid
-  script: grid_all_loadCaseRotation/test.py
-  except:
-    - master
-    - release
-
 grid_all_restartMPI:
   stage: grid
   script:

PRIVATE

@@ -1 +1 @@
-Subproject commit c92f6d3e23a4c310898b502f00e395dbe670a63c
+Subproject commit dde6a5836089b14bd39d4393a47b82b351d2bd85

examples/ConfigFiles/Kinematics_Hydrogen_Strain.config

@@ -1,2 +0,0 @@
-(kinematics) vacancy_strain
-vacancy_strain_coeff            0.006

examples/SpectralMethod/Polycrystal/20grains16x16x16.geom

@@ -1,262 +0,0 @@
-5	header
-grid	a 16	b 16	c 16
-size	x 1.000000	y 1.000000	z 1.000000
-origin	x 0.000000	y 0.000000	z 0.000000
-microstructures 20
-homogenization	1
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- 4  4  4  4  1  1  1  1  1 15 15 15 15 15  3  3
- 3  4  4  1  1  1  1  1  1 15 15  3  3  3  3  3
-10 10  1  1  1  1  1  1  3  3  3  3  3  3  3  3
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- 3  4  4  4  1  1  1  1  1 15 15 15 15  3  3  3
-13 13  4  1  1  1  1  1  1 15  3  3  3  3  3  3
-13 13 13  1  1  1  1  1  3  3  3  3  3  3  3  3
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- 2  2  2  2  2  2  2  2  7  7  7  7  7  7  7 19
- 2  2  2  2  2  2  2  4  4 15  7  7  7 19 19 19
-19  2  2  2  2  4  4  4  1 15 15 15 19 19 19 19

examples/SpectralMethod/Polycrystal/20grains16x16x16.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <RectilinearGrid WholeExtent="0 16 0 16 0 16">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="2" format="binary">
+        AQAAAACAAAAkAAAALAAAAA==eF7LzUwuyi8uKSpNLiktSi1WMDJgyMjPzU9PzcusSizJzM/jNGQAAASkDSY=
+      </Array>
+    </FieldData>
+  <Piece Extent="0 16 0 16 0 16">
+    <PointData>
+    </PointData>
+    <CellData>
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="0" RangeMax="19">
+        AQAAAACAAAAAAAAADwYAAA==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
+      </DataArray>
+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
+        AQAAAACAAACIAAAAOAAAAA==eF5jYEAGG+wh9AEofQJKX4DSV6D0DSh9B0o/gNKPoPQTKP0MSr+A0q+g9Bso/Q5Kf7AHAB2kEak=
+      </DataArray>
+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
+        AQAAAACAAACIAAAAOAAAAA==eF5jYEAGG+wh9AEofQJKX4DSV6D0DSh9B0o/gNKPoPQTKP0MSr+A0q+g9Bso/Q5Kf7AHAB2kEak=
+      </DataArray>
+      <DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
+        AQAAAACAAACIAAAAOAAAAA==eF5jYEAGG+wh9AEofQJKX4DSV6D0DSh9B0o/gNKPoPQTKP0MSr+A0q+g9Bso/Q5Kf7AHAB2kEak=
+      </DataArray>
+    </Coordinates>
+  </Piece>
+  </RectilinearGrid>
+</VTKFile>

processing/pre/geom_fromDREAM3D.py

@@ -68,4 +68,4 @@ for name in filenames:
     geom = damask.Geom.load_DREAM3D(name,options.basegroup,options.pointwise)
     damask.util.croak(geom)
 
-    geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False)
+    geom.save_ASCII(os.path.splitext(name)[0]+'.geom')

processing/pre/geom_fromMinimalSurface.py

@@ -66,4 +66,4 @@ geom=damask.Geom.from_minimal_surface(options.grid,options.size,options.type,opt
                                       options.periods,options.microstructure)
 damask.util.croak(geom)
 
-geom.save_ASCII(sys.stdout if name is None else name,compress=False)
+geom.save_ASCII(sys.stdout if name is None else name)

processing/pre/geom_fromOsteonGeometry.py

@@ -138,4 +138,4 @@ geom = damask.Geom(microstructure.reshape(grid),
                    comments=header)
 damask.util.croak(geom)
 
-geom.save_ASCII(sys.stdout if name is None else name,compress=False)
+geom.save_ASCII(sys.stdout if name is None else name)

processing/pre/geom_fromTable.py

@@ -54,4 +54,4 @@ for name in filenames:
     geom = damask.Geom.from_table(t,options.pos,labels)
     damask.util.croak(geom)
 
-    geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False)
+    geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom')

processing/pre/geom_grainGrowth.py

@@ -174,4 +174,4 @@ for name in filenames:
               origin    = geom.origin,
               comments  = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
              )\
-        .save_ASCII(sys.stdout if name is None else name,compress=False)
+        .save_ASCII(sys.stdout if name is None else name)

python/damask/_geom.py

@@ -320,7 +320,7 @@ class Geom:
         else:
             material_ = material_.reshape(grid)
 
-        return Geom(material = material_+1 if material is None else material[material_],
+        return Geom(material = material_ if material is None else material[material_],
                     size     = size,
                     comments = util.execution_stamp('Geom','from_Laguerre_tessellation'),
                    )
@@ -350,7 +350,7 @@ class Geom:
         KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
         devNull,material_ = KDTree.query(coords)
 
-        return Geom(material = (material_+1 if material is None else material[material_]).reshape(grid),
+        return Geom(material = (material_ if material is None else material[material_]).reshape(grid),
                     size     = size,
                     comments = util.execution_stamp('Geom','from_Voronoi_tessellation'),
                    )
@@ -399,7 +399,7 @@ class Geom:
 
 
     @staticmethod
-    def from_minimal_surface(grid,size,surface,threshold=0.0,periods=1,materials=(1,2)):
+    def from_minimal_surface(grid,size,surface,threshold=0.0,periods=1,materials=(0,1)):
         """
         Generate geometry from definition of triply periodic minimal surface.
 
@@ -467,9 +467,8 @@ class Geom:
 
         Parameters
         ----------
-        fname : str, optional
+        fname : str or or pathlib.Path
-            Filename to write. If no file is given, a string is returned.
+            Filename to write. Valid extension is .vtr, it will be appended if not given.
-            Valid extension is .vtr, it will be appended if not given.
         compress : bool, optional
             Compress with zlib algorithm. Defaults to True.
 
@@ -481,9 +480,9 @@ class Geom:
         v.save(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr',parallel=False,compress=compress)
 
 
-    def save_ASCII(self,fname,compress=None):
+    def save_ASCII(self,fname):
         """
-        Writes a geom file.
+        Write a geom file.
 
         Parameters
         ----------
@@ -500,57 +499,11 @@ class Geom:
                    'homogenization 1',
                   ]
 
-        grid = self.grid
+        format_string = '%g' if self.material.dtype in np.sctypes['float'] else \
-
+                        '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.material)))))
-        if compress is None:
+        np.savetxt(fname,
-            plain = grid.prod()/self.N_materials < 250
+                   self.material.reshape([self.grid[0],np.prod(self.grid[1:])],order='F').T,
-        else:
+                   header='\n'.join(header), fmt=format_string, comments='')
-            plain = not compress
-
-        if plain:
-            format_string = '%g' if self.material.dtype in np.sctypes['float'] else \
-                            '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.material)))))
-            np.savetxt(fname,
-                       self.material.reshape([grid[0],np.prod(grid[1:])],order='F').T,
-                       header='\n'.join(header), fmt=format_string, comments='')
-        else:
-            try:
-                f = open(fname,'w')
-            except TypeError:
-                f = fname
-
-            compressType = None
-            former = start = -1
-            reps = 0
-            for current in self.material.flatten('F'):
-                if abs(current - former) == 1 and (start - current) == reps*(former - current):
-                    compressType = 'to'
-                    reps += 1
-                elif current == former and start == former:
-                    compressType = 'of'
-                    reps += 1
-                else:
-                    if   compressType is None:
-                        f.write('\n'.join(header)+'\n')
-                    elif compressType == '.':
-                        f.write(f'{former}\n')
-                    elif compressType == 'to':
-                        f.write(f'{start} to {former}\n')
-                    elif compressType == 'of':
-                        f.write(f'{reps} of {former}\n')
-
-                    compressType = '.'
-                    start = current
-                    reps = 1
-
-                former = current
-
-            if compressType == '.':
-                f.write(f'{former}\n')
-            elif compressType == 'to':
-                f.write(f'{start} to {former}\n')
-            elif compressType == 'of':
-                f.write(f'{reps} of {former}\n')
 
 
     def show(self):
@@ -562,7 +515,7 @@ class Geom:
     def add_primitive(self,dimension,center,exponent,
                       fill=None,R=Rotation(),inverse=False,periodic=True):
         """
-        Inserts a primitive geometric object at a given position.
+        Insert a primitive geometric object at a given position.
 
         Parameters
         ----------

python/tests/reference/Geom/clean_2_1+2+3_False.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_2_1+2+3_True.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_2_1_False.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_2_1_True.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_2_None_False.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_2_None_True.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_3_1+2+3_False.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_3_1+2+3_True.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_3_1_False.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_3_1_True.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_3_None_False.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_3_None_True.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_4_1+2+3_False.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
       </Array>
     </FieldData>
   <Piece Extent="0 8 0 5 0 4">

python/tests/reference/Geom/clean_4_1+2+3_True.vtr

@@ -3,7 +3,7 @@
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
     <FieldData>
       <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
-        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
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python/tests/reference/Geom/clean_4_1_False.vtr

@@ -3,7 +3,7 @@
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     <FieldData>
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python/tests/reference/Geom/clean_4_1_True.vtr

@@ -3,7 +3,7 @@
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     <FieldData>
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python/tests/reference/Geom/clean_4_None_False.vtr

@@ -3,7 +3,7 @@
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     <FieldData>
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python/tests/reference/Geom/clean_4_None_True.vtr

@@ -3,7 +3,7 @@
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python/tests/reference/Geom/flip_directions=x-y-z.geom

@@ -1,25 +0,0 @@
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- 1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1

python/tests/reference/Geom/flip_directions=x.geom

@@ -1,25 +0,0 @@
-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
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- 2  2  2  2  2  2  2  2
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- 2  2  2  2  2  2  2  2
- 2  2  2  2  2  2  2  2
- 8  7  6  5  4  3  2  1
-16 15 14 13 12 11 10  9
-24 23 22 21 20 19 18 17
-32 31 30 29 28 27 26 25
-40 39 38 37 36 35 34 33

python/tests/reference/Geom/flip_directions=y-z.geom

@@ -1,25 +0,0 @@
-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
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- 1  2  3  4  5  6  7  8
- 2  2  2  2  2  2  2  2
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- 2  2  2  2  2  2  2  2
- 2  2  2  2  2  2  2  2
- 2  2  2  2  2  2  2  2
-34 35 36 37 38 39 40 41
-26 27 28 29 30 31 32 33
-18 19 20 21 22 23 24 25
-10 11 12 13 14 15 16 17
- 2  3  4  5  6  7  8  9
- 1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1

python/tests/reference/Geom/flip_directions=z-x-y.geom

@@ -1,25 +0,0 @@
-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
-40 39 38 37 36 35 34 33
-32 31 30 29 28 27 26 25
-24 23 22 21 20 19 18 17
-16 15 14 13 12 11 10  9
- 8  7  6  5  4  3  2  1
- 2  2  2  2  2  2  2  2
- 2  2  2  2  2  2  2  2
- 2  2  2  2  2  2  2  2
- 2  2  2  2  2  2  2  2
- 2  2  2  2  2  2  2  2
-41 40 39 38 37 36 35 34
-33 32 31 30 29 28 27 26
-25 24 23 22 21 20 19 18
-17 16 15 14 13 12 11 10
- 9  8  7  6  5  4  3  2
- 1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1

python/tests/reference/Geom/flip_directions_x-y-z.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
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+      </Array>
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+  <Piece Extent="0 8 0 5 0 4">
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+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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+      <DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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+  </Piece>
+  </RectilinearGrid>
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python/tests/reference/Geom/flip_directions_x.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <RectilinearGrid WholeExtent="0 8 0 5 0 4">
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+      </Array>
+    </FieldData>
+  <Piece Extent="0 8 0 5 0 4">
+    <PointData>
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+    <CellData>
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
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+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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+      </DataArray>
+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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+      <DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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+  </Piece>
+  </RectilinearGrid>
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python/tests/reference/Geom/flip_directions_y-z.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <RectilinearGrid WholeExtent="0 8 0 5 0 4">
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+      </Array>
+    </FieldData>
+  <Piece Extent="0 8 0 5 0 4">
+    <PointData>
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+    <CellData>
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+      </DataArray>
+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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+      </DataArray>
+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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+      </DataArray>
+      <DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
+        AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
+      </DataArray>
+    </Coordinates>
+  </Piece>
+  </RectilinearGrid>
+</VTKFile>

python/tests/reference/Geom/flip_directions_z-x-y.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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+      </Array>
+    </FieldData>
+  <Piece Extent="0 8 0 5 0 4">
+    <PointData>
+    </PointData>
+    <CellData>
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
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+      </DataArray>
+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
+        AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
+      </DataArray>
+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
+        AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
+      </DataArray>
+      <DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
+        AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
+      </DataArray>
+    </Coordinates>
+  </Piece>
+  </RectilinearGrid>
+</VTKFile>

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

@@ -1,85 +0,0 @@
-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  1  1  1  1  1  1  1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
- 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
- 2  3  4  5  6  7  8  9  9  8  7  6  5  4  3  2
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-34 35 36 37 38 39 40 41 41 40 39 38 37 36 35 34
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-26 27 28 29 30 31 32 33 33 32 31 30 29 28 27 26
-18 19 20 21 22 23 24 25 25 24 23 22 21 20 19 18
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- 2  3  4  5  6  7  8  9  9  8  7  6  5  4  3  2
- 2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2
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- 1  2  3  4  5  6  7  8  8  7  6  5  4  3  2  1
- 1  2  3  4  5  6  7  8  8  7  6  5  4  3  2  1
- 9 10 11 12 13 14 15 16 16 15 14 13 12 11 10  9
-17 18 19 20 21 22 23 24 24 23 22 21 20 19 18 17
-25 26 27 28 29 30 31 32 32 31 30 29 28 27 26 25
-33 34 35 36 37 38 39 40 40 39 38 37 36 35 34 33
-33 34 35 36 37 38 39 40 40 39 38 37 36 35 34 33
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-17 18 19 20 21 22 23 24 24 23 22 21 20 19 18 17
- 9 10 11 12 13 14 15 16 16 15 14 13 12 11 10  9
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python/tests/reference/Geom/mirror_directions=x_reflect=False.geom

@@ -1,25 +0,0 @@
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python/tests/reference/Geom/mirror_directions=y-z_reflect=False.geom

@@ -1,53 +0,0 @@
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python/tests/reference/Geom/mirror_directions=z-x-y_reflect=False.geom

@@ -1,53 +0,0 @@
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python/tests/reference/Geom/mirror_directions_x+reflect_False.vtr

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python/tests/reference/Geom/mirror_directions_x-y-z+reflect_True.vtr

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python/tests/reference/Geom/mirror_directions_y-z+reflect_False.vtr

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python/tests/reference/Geom/mirror_directions_z-x-y+reflect_False.vtr

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python/tests/reference/Geom/rotate_Eulers=0.0-32.0-240.0.geom

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python/tests/reference/Geom/rotate_Eulers=32.0-68.0-21.0.geom

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-grid   a 11 b 11 c 9
-size   x 1.1e-05 y 1.1000000000000001e-05 z 9e-06
-origin x -1.5e-06 y -3.0000000000000005e-06 z -2.4999999999999998e-06
-homogenization 1
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python/tests/reference/Geom/rotate_Eulers_0.0-32.0-240.0.vtr

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python/tests/reference/Geom/rotate_Eulers_32.0-68.0-21.0.vtr

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python/tests/reference/Geom/scale_grid=10-10-10.geom

@@ -1,105 +0,0 @@
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python/tests/reference/Geom/scale_grid=10-11-10.geom

@@ -1,115 +0,0 @@
-4 header
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-size   x 8e-06 y 5e-06 z 4e-06
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-homogenization 1
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python/tests/reference/Geom/scale_grid=10-13-10.geom

@@ -1,135 +0,0 @@
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python/tests/reference/Geom/scale_grid=10-20-2.geom

@@ -1,45 +0,0 @@
-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
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python/tests/reference/Geom/scale_grid=5-4-20.geom

@@ -1,85 +0,0 @@
-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
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python/tests/reference/Geom/scale_grid=8-10-12.geom

@@ -1,125 +0,0 @@
-4 header
-grid   a 8 b 10 c 12
-size   x 8e-06 y 5e-06 z 4e-06
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-homogenization 1
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python/tests/reference/Geom/scale_grid_10-10-10.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <RectilinearGrid WholeExtent="0 10 0 10 0 10">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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+      </Array>
+    </FieldData>
+  <Piece Extent="0 10 0 10 0 10">
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+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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+      </DataArray>
+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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+      </DataArray>
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+      </DataArray>
+    </Coordinates>
+  </Piece>
+  </RectilinearGrid>
+</VTKFile>

python/tests/reference/Geom/scale_grid_10-11-10.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <RectilinearGrid WholeExtent="0 10 0 11 0 10">
+    <FieldData>
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+      </Array>
+    </FieldData>
+  <Piece Extent="0 10 0 11 0 10">
+    <PointData>
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+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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+      </DataArray>
+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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+      </DataArray>
+      <DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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+      </DataArray>
+    </Coordinates>
+  </Piece>
+  </RectilinearGrid>
+</VTKFile>

python/tests/reference/Geom/scale_grid_10-13-10.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <RectilinearGrid WholeExtent="0 10 0 13 0 10">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9UrTk7MSVUos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFYKEKs=
+      </Array>
+    </FieldData>
+  <Piece Extent="0 10 0 13 0 10">
+    <PointData>
+    </PointData>
+    <CellData>
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
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+      </DataArray>
+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
+        AQAAAACAAABYAAAARQAAAA==eF5jYIAAj/V7Zn26vsoOQu+yK2vm/fJV8QiUf8qu9+3WBd+PXYCKX7GLl0x1/1JzHSp/y87QVeTdB6N7UHUP7ACC9C8w
+      </DataArray>
+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
+        AQAAAACAAABwAAAAWgAAAA==eF5jYICA8tytkUvOz7SD0CvtJIU8nHdHb4byd9plpQjuOKZ4ACp+2O7E/rpz66ceg8qftFOTfvNkBudZqLoLdk671/w9sO8iVP1lu48Zjzu2/rhiBwBjSjRO
+      </DataArray>
+      <DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
+        AQAAAACAAABYAAAARQAAAA==eF5jYIAAj/V7Zn26PssOQq+yK2vm/fJVcQuUv8uu9+3WBd+PHYCKH7GLl0x1/1JzHCp/ys7QVeTdB6NzUHUX7ABrNC6Q
+      </DataArray>
+    </Coordinates>
+  </Piece>
+  </RectilinearGrid>
+</VTKFile>

python/tests/reference/Geom/scale_grid_10-20-2.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <RectilinearGrid WholeExtent="0 10 0 20 0 2">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9UrTk7MSVUos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFYKEKs=
+      </Array>
+    </FieldData>
+  <Piece Extent="0 10 0 20 0 2">
+    <PointData>
+    </PointData>
+    <CellData>
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="40">
+        AQAAAACAAACADAAAdgAAAA==eF7tzMsWgQAYReEuKJUoRKGLS3n/JzSwJ51ZRq3l35Nvtl3nm2uapmmaP+ihLy5wiSsxwBDn/ltjhLGY4AZTcYs7tN/Yqb8Mc9yLBzxiIZ7wjP/2K7HCi3jFG9Zigy3ab+zUX4d3fIhPfGEvDvjGuf8+MEUQzQ==
+      </DataArray>
+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
+        AQAAAACAAABYAAAARQAAAA==eF5jYIAAj/V7Zn26vsoOQu+yK2vm/fJV8QiUf8qu9+3WBd+PXYCKX7GLl0x1/1JzHSp/y87QVeTdB6N7UHUP7ACC9C8w
+      </DataArray>
+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
+        AQAAAACAAACoAAAAgQAAAA==eF5jYICAvrdbF3w/NsEOQi+wC30iUFistRLK32D3KeNxx9YfW6DiO+12xNtFGsbshcofsHNYfWbKtfuHoOqO2C1W+1UzRfA4VP1JO/ZF6qlBzqeh+s7aZcmG+gqUnofqv2CX7nNQKv3yRag5l+wkuW7wub25bPcRbN4VOwAdV1bT
+      </DataArray>
+      <DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
+        AQAAAACAAAAYAAAAGAAAAA==eF5jYICA3rdbF3w/dsAOQl+wAwBg4gsl
+      </DataArray>
+    </Coordinates>
+  </Piece>
+  </RectilinearGrid>
+</VTKFile>

python/tests/reference/Geom/scale_grid_5-4-20.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <RectilinearGrid WholeExtent="0 5 0 4 0 20">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9UrTk7MSVUos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFYKEKs=
+      </Array>
+    </FieldData>
+  <Piece Extent="0 5 0 4 0 20">
+    <PointData>
+    </PointData>
+    <CellData>
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
+        AQAAAACAAACADAAAeAAAAA==eF7t1TkWggAUQ1EREZS5BFQmB9j/Bin++40b8OBJmtumSoKDJZDyBx7xhGeM8YJXzLDAEmts8YYP7HHECZ/4xg+uqH4W9bOon+W7n5Ryf/oPhxih70yCvjMp5ug7U2GDHd7Rd2ZA35kZX+g7s6D6Wf613wZ8oBHR
+      </DataArray>
+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
+        AQAAAACAAAAwAAAALAAAAA==eF5jYIAAj/V7Zn26vssOQp+yK2vm/fJV8QqUf8uu9+3WBd+PPbADAPj2GSc=
+      </DataArray>
+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
+        AQAAAACAAAAoAAAAIwAAAA==eF5jYICAjxmPO7b+2GIHoY/YZcmG+gqUnofyr9gBAEcwExU=
+      </DataArray>
+      <DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
+        AQAAAACAAACoAAAAfwAAAA==eF5jYIAAj/V7Zn263mUHoWfZlTXzfvmquATKX2XX+3brgu/HNkDFt9jFS6a6f6nZDpXfZWfoKvLug9E+qLoDdk07Ek+VlRyCqj9il+W3U7b0/FGovuN2IU8ECou1TkL1n7Kzqco4Uth6BmrOOTs1gQPiBQ/OQ827YAcA/NFWxg==
+      </DataArray>
+    </Coordinates>
+  </Piece>
+  </RectilinearGrid>
+</VTKFile>

python/tests/reference/Geom/scale_grid_8-10-12.vtr

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <RectilinearGrid WholeExtent="0 8 0 10 0 12">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9UrTk7MSVUos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFYKEKs=
+      </Array>
+    </FieldData>
+  <Piece Extent="0 8 0 10 0 12">
+    <PointData>
+    </PointData>
+    <CellData>
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
+        AQAAAACAAAAAHgAAyAAAAA==eF7t2LcBAkEUxFDu8N5776H/BglQBwpvNnmRskn+FrX/K2KMsWKWWMcGNrGFbexgF23fwz4OcIgjHOMEp2j7Gc5xgUtc4Ro3uEXb73CPBzziCc94wSva/oZ3fOATX/jGD37R9nY/trf7sb3dj+3tfmxv92N7ux/b2/3Y3u7H9nY/trf7sb3dj+3tfmxv92N7ux/b2/3YvowxxhhjjJXS/gPa3t4htrd3iO3tHWJ7e4fY3u7H9nY/trf7sb3dj+3tfmz/A1V7KtE=
+      </DataArray>
+    </CellData>
+    <Coordinates>
+      <DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
+        AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
+      </DataArray>
+      <DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
+        AQAAAACAAABYAAAASAAAAA==eF5jYICAvrdbF3w/tsAOQm+wC30iUFistRPKP2D3KeNxx9YfR6DiJ+12xNtFGsachcpfsHNYfWbKtfuX7D6C1V2xAwCgPTAG
+      </DataArray>
+      <DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
+        AQAAAACAAABoAAAAUQAAAA==eF5jYIAAwUmfGubHTbOD0Mvset9uXfD92AYof5vdVDP9RPdvu6HiB+zO21+ZcHrSYaj8MbvgJwKFxVonoepO213v8A2UPnQOqv6CHQDLvTPb
+      </DataArray>
+    </Coordinates>
+  </Piece>
+  </RectilinearGrid>
+</VTKFile>

python/tests/test_Geom.py

@@ -1,6 +1,3 @@
-import os
-import time
-
 import pytest
 import numpy as np
 
@@ -33,6 +30,10 @@ def reference_dir(reference_dir_base):
 
 class TestGeom:
 
+    @pytest.fixture(autouse=True)
+    def _execution_stamp(self, execution_stamp):
+        print('patched damask.util.execution_stamp')
+
     def test_diff_equal(self,default):
         assert str(default.diff(default)) == ''
 
@@ -42,44 +43,14 @@ class TestGeom:
         assert str(default.diff(new)) != ''
 
 
-    def test_write_read_str(self,default,tmp_path):
-        default.save_ASCII(str(tmp_path/'default.geom'))
-        new = Geom.load_ASCII(str(tmp_path/'default.geom'))
-        assert geom_equal(default,new)
-
-
-    def test_write_read_file(self,default,tmp_path):
-        with open(tmp_path/'default.geom','w') as f:
-            default.save_ASCII(f,compress=True)
-        with open(tmp_path/'default.geom') as f:
-            new = Geom.load_ASCII(f)
-        assert geom_equal(default,new)
-
-
     def test_read_write_vtr(self,default,tmp_path):
         default.save(tmp_path/'default')
-        for _ in range(10):
-            time.sleep(.2)
-            if os.path.exists(tmp_path/'default.vtr'): break
-
         new = Geom.load(tmp_path/'default.vtr')
         assert geom_equal(new,default)
 
-
-    def test_invalid_geom(self,tmp_path):
-        with open(tmp_path/'invalid_file','w') as f:
-            f.write('this is not a valid header')
-        with open(tmp_path/'invalid_file','r') as f:
-            with pytest.raises(TypeError):
-                Geom.load_ASCII(f)
-
-
     def test_invalid_vtr(self,tmp_path):
         v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
         v.save(tmp_path/'no_materialpoint.vtr')
-        for _ in range(10):
-            time.sleep(.2)
-            if os.path.exists(tmp_path/'no_materialpoint.vtr'): break
         with pytest.raises(ValueError):
             Geom.load(tmp_path/'no_materialpoint.vtr')
 
@@ -91,13 +62,6 @@ class TestGeom:
         g = Geom(np.zeros((3,3,3)),np.ones(3))
         assert g.material.dtype in np.sctypes['int']
 
-    @pytest.mark.parametrize('compress',[True,False])
-    def test_compress(self,default,tmp_path,compress):
-        default.save_ASCII(tmp_path/'default.geom',compress=compress)
-        new = Geom.load_ASCII(tmp_path/'default.geom')
-        assert geom_equal(new,default)
-
-
     def test_invalid_size(self,default):
         with pytest.raises(ValueError):
             Geom(default.material[1:,1:,1:],
@@ -133,10 +97,10 @@ class TestGeom:
                             )
     def test_mirror(self,default,update,reference_dir,directions,reflect):
         modified = default.mirror(directions,reflect)
-        tag = f'directions={"-".join(directions)}_reflect={reflect}'
+        tag = f'directions_{"-".join(directions)}+reflect_{reflect}'
-        reference = reference_dir/f'mirror_{tag}.geom'
+        reference = reference_dir/f'mirror_{tag}.vtr'
-        if update: modified.save_ASCII(reference)
+        if update: modified.save(reference)
-        assert geom_equal(Geom.load_ASCII(reference),
+        assert geom_equal(Geom.load(reference),
                           modified)
 
 
@@ -155,10 +119,10 @@ class TestGeom:
                             )
     def test_flip(self,default,update,reference_dir,directions):
         modified = default.flip(directions)
-        tag = f'directions={"-".join(directions)}'
+        tag = f'directions_{"-".join(directions)}'
-        reference = reference_dir/f'flip_{tag}.geom'
+        reference = reference_dir/f'flip_{tag}.vtr'
-        if update: modified.save_ASCII(reference)
+        if update: modified.save(reference)
-        assert geom_equal(Geom.load_ASCII(reference),
+        assert geom_equal(Geom.load(reference),
                           modified)
 
 
@@ -185,9 +149,6 @@ class TestGeom:
         reference = reference_dir/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
         if update and stencil > 1:
             current.save(reference)
-            for _ in range(10):
-                time.sleep(.2)
-                if os.path.exists(reference.with_suffix('.vtr')): break
         assert geom_equal(Geom.load(reference) if stencil > 1 else default,
                           current
                          )
@@ -204,10 +165,10 @@ class TestGeom:
                             )
     def test_scale(self,default,update,reference_dir,grid):
         modified = default.scale(grid)
-        tag = f'grid={util.srepr(grid,"-")}'
+        tag = f'grid_{util.srepr(grid,"-")}'
-        reference = reference_dir/f'scale_{tag}.geom'
+        reference = reference_dir/f'scale_{tag}.vtr'
-        if update: modified.save_ASCII(reference)
+        if update: modified.save(reference)
-        assert geom_equal(Geom.load_ASCII(reference),
+        assert geom_equal(Geom.load(reference),
                           modified)
 
 
@@ -247,10 +208,10 @@ class TestGeom:
                                        [0.0,32.0,240.0]])
     def test_rotate(self,default,update,reference_dir,Eulers):
         modified = default.rotate(Rotation.from_Eulers(Eulers,degrees=True))
-        tag = f'Eulers={util.srepr(Eulers,"-")}'
+        tag = f'Eulers_{util.srepr(Eulers,"-")}'
-        reference = reference_dir/f'rotate_{tag}.geom'
+        reference = reference_dir/f'rotate_{tag}.vtr'
-        if update: modified.save_ASCII(reference)
+        if update: modified.save(reference)
-        assert geom_equal(Geom.load_ASCII(reference),
+        assert geom_equal(Geom.load(reference),
                           modified)
 
 
@@ -342,8 +303,8 @@ class TestGeom:
         N_seeds= np.random.randint(10,30)
         seeds  = np.random.rand(N_seeds,3) * np.broadcast_to(size,(N_seeds,3))
         weights= np.full((N_seeds),-np.inf)
-        ms     = np.random.randint(1, N_seeds+1)
+        ms     = np.random.randint(N_seeds)
-        weights[ms-1] = np.random.random()
+        weights[ms] = np.random.random()
         Laguerre = Geom.from_Laguerre_tessellation(grid,size,seeds,weights,periodic=np.random.random()>0.5)
         assert np.all(Laguerre.material == ms)
 
@@ -353,8 +314,8 @@ class TestGeom:
         grid  = np.random.randint(5,10,3)*2
         size  = grid.astype(np.float)
         seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
-        material = np.ones(grid)
+        material = np.zeros(grid)
-        material[:,grid[1]//2:,:] = 2
+        material[:,grid[1]//2:,:] = 1
         if   approach == 'Laguerre':
             geom = Geom.from_Laguerre_tessellation(grid,size,seeds,np.ones(2),periodic=np.random.random()>0.5)
         elif approach == 'Voronoi':

src/grid/discretization_grid.f90

@@ -67,11 +67,7 @@ subroutine discretization_grid_init(restart)
 
   print'(/,a)', ' <<<+-  discretization_grid init  -+>>>'; flush(IO_STDOUT)
 
-  if(index(interface_geomFile,'.vtr') /= 0) then
+  call readVTR(grid,geomSize,origin,materialAt)
-    call readVTR(grid,geomSize,origin,materialAt)
-  else
-    call readGeom(grid,geomSize,origin,materialAt)
-  endif
 
   print'(/,a,3(i12  ))',  ' grid     a b c: ', grid
   print'(a,3(es12.5))',   ' size     x y z: ', geomSize
@@ -412,11 +408,12 @@ subroutine readVTR(grid,geomSize,origin,material)
     startPos = endPos + 2_pI64
 
   end do
-
+  material = material + 1
   if(.not. allocated(material))       call IO_error(error_ID = 844, ext_msg='material data not found')
   if(size(material) /= product(grid)) call IO_error(error_ID = 844, ext_msg='size(material)')
   if(any(geomSize<=0))                call IO_error(error_ID = 844, ext_msg='size')
   if(any(grid<1))                     call IO_error(error_ID = 844, ext_msg='grid')
+  if(any(material<0))                 call IO_error(error_ID = 844, ext_msg='material ID < 0')
 
   contains