Merge remote-tracking branch 'origin/development' into unit-in-vtk

PRIVATE

@@ -1 +1 @@
-Subproject commit e719eee4f213baedecb8c68afab12331e3730d62
+Subproject commit 25b7b78951ab9fb682aaf048d3e0f0d09a3be695

VERSION

@@ -1 +1 @@
-v3.0.0-alpha-782-ga0b6c2690
+v3.0.0-alpha-801-g7356330cf

processing/pre/geom_grainGrowth.py

@@ -15,8 +15,8 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 
-getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0)                               # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
-struc = ndimage.generate_binary_structure(3,1)                                                     # 3D von Neumann neighborhood
+getInterfaceEnergy = lambda A,B: np.float32((A != B)*1.0)                                           # 1.0 if A & B are distinct, 0.0 otherwise
+struc = ndimage.generate_binary_structure(3,1)                                                      # 3D von Neumann neighborhood
 
 
 #--------------------------------------------------------------------------------------------------
@@ -62,7 +62,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
   damask.util.report(scriptName,name)
 
-  geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+  geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
   grid_original = geom.grid
   damask.util.croak(geom)
@@ -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)
+        .save(sys.stdout if name is None else name)

processing/pre/mentat_pbcOnBoxMesh.py

@@ -11,8 +11,6 @@ import numpy as np
 
 import damask
 
-sys.path.append(str(damask.solver.Marc().library_path))
-
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
@@ -235,6 +233,7 @@ if remote and filenames != []:
 if filenames == []: filenames = [None]
 
 if remote:
+  sys.path.append(str(damask.solver.Marc().library_path))
   import py_mentat
 
   damask.util.report(scriptName, 'waiting to connect...')

processing/pre/mentat_spectralBox.py

@@ -9,7 +9,6 @@ import damask
 
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
-sys.path.append(str(damask.solver.Marc().library_path))
 
 #-------------------------------------------------------------------------------------------------
 def outMentat(cmd,locals):
@@ -185,9 +184,10 @@ parser.set_defaults(port = None,
 
 if options.port is not None:
     try:
+        sys.path.append(str(damask.solver.Marc().library_path))
         import py_mentat
     except ImportError:
-        parser.error('no valid Mentat release found.')
+        parser.error('no valid Mentat release found')
 
 # --- loop over input files ------------------------------------------------------------------------
 
@@ -196,7 +196,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     material = geom.material.flatten(order='F')
 
     cmds = [\

python/damask/_geom.py

@@ -213,9 +213,8 @@ class Geom:
         if not keyword.startswith('head') or header_length < 3:
             raise TypeError('Header length information missing or invalid')
 
-        content = f.readlines()
-
         comments = []
+        content = f.readlines()
         for i,line in enumerate(content[:header_length]):
             items = line.split('#')[0].lower().strip().split()
             key = items[0] if items else ''
@@ -228,7 +227,7 @@ class Geom:
             else:
                 comments.append(line.strip())
 
-        material = np.empty(grid.prod())                                                      # initialize as flat array
+        material = np.empty(grid.prod())                                                            # initialize as flat array
         i = 0
         for line in content[header_length:]:
             items = line.split('#')[0].split()
@@ -246,8 +245,8 @@ class Geom:
         if i != grid.prod():
             raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
 
-        if not np.any(np.mod(material,1) != 0.0):                                             # no float present
-            material = material.astype('int')
+        if not np.any(np.mod(material,1) != 0.0):                                                   # no float present
+            material = material.astype('int') - (1 if material.min() > 0 else 0)
 
         return Geom(material.reshape(grid,order='F'),size,origin,comments)
 
@@ -510,7 +509,7 @@ class Geom:
 
         Parameters
         ----------
-        fname : str or or pathlib.Path
+        fname : str or pathlib.Path
             Filename to write. Valid extension is .vtr, it will be appended if not given.
         compress : bool, optional
             Compress with zlib algorithm. Defaults to True.

python/tests/test_Geom.py

@@ -74,6 +74,7 @@ class TestGeom:
 
     def test_save_load_ASCII(self,default,tmp_path):
         default.save_ASCII(tmp_path/'ASCII')
+        default.material -= 1
         assert geom_equal(Geom.load_ASCII(tmp_path/'ASCII'),default)
 
     def test_invalid_origin(self,default):