Merge branch 'misc-improvements' into 'development'

a number of small changes

See merge request damask/DAMASK!428

.gitlab-ci.yml

@@ -102,13 +102,6 @@ processing:
     - master
     - release
 
-###################################################################################################
-preprocessing_deprecated:
-  stage: python
-  script: PreProcessing/test.py
-  except:
-    - master
-    - release
 
 ###################################################################################################
 compile_grid_Intel:

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.10.0)
+cmake_minimum_required (VERSION 3.12.0)
 include (FindPkgConfig REQUIRED)
 
 if (DEFINED ENV{PETSC_DIR})
@@ -31,6 +31,7 @@ message ("\nBuilding ${CMAKE_PROJECT_NAME} ${DAMASK_VERSION}\n")
 
 add_definitions (-DPETSC)
 add_definitions (-DDAMASKVERSION="${DAMASK_VERSION}")
+add_definitions (-DCMAKE_SYSTEM="${CMAKE_SYSTEM}")
 
 if (CMAKE_BUILD_TYPE STREQUAL "")
     set (CMAKE_BUILD_TYPE "RELEASE")

DAMASK_prerequisites.sh

@@ -74,7 +74,7 @@ echo PETSC_ARCH: $PETSC_ARCH
 echo PETSC_DIR: $PETSC_DIR
 echo
 echo $PETSC_DIR/$PETSC_ARCH/lib:
-/s $PETSC_DIR/$PETSC_ARCH/lib
+ls $PETSC_DIR/$PETSC_ARCH/lib
 echo
 echo $PETSC_DIR/$PETSC_ARCH/lib/petsc/conf/petscvariables:
 cat $PETSC_DIR/$PETSC_ARCH/lib/petsc/conf/petscvariables

PRIVATE

@@ -1 +1 @@
-Subproject commit 6037ed541710fc84699ee2ca1d36a69d7fa20f0f
+Subproject commit 36ac61caef1eec1ac68cadbed1a8f6f07a035f54

python/damask/_config.py

@@ -146,12 +146,6 @@ class Config(dict):
         if 'sort_keys' not in kwargs:
             kwargs['sort_keys'] = False
 
-        def array_representer(dumper, data):
-            """Convert numpy array to list of native types."""
-            return dumper.represent_list([d.item() for d in data])
-
-        NiceDumper.add_representer(np.ndarray, array_representer)
-
         try:
             fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
         except TypeError:                                                                           # compatibility with old pyyaml

python/damask/_result.py

@@ -567,9 +567,13 @@ class Result:
         formula = kwargs['formula']
         for d in re.findall(r'#(.*?)#',formula):
             formula = formula.replace(f'#{d}#',f"kwargs['{d}']['data']")
+        data = eval(formula)
+
+        if not hasattr(data,'shape') or data.shape[0] != kwargs[d]['data'].shape[0]:
+            raise ValueError("'{}' results in invalid shape".format(kwargs['formula']))
 
         return {
-                'data':  eval(formula),
+                'data':  data,
                 'label': kwargs['label'],
                 'meta':  {
                           'unit':        kwargs['unit'],

python/damask/mechanics.py

@@ -257,18 +257,18 @@ def _polar_decomposition(T,requested):
     u, _, vh = _np.linalg.svd(T)
     R = _np.einsum('...ij,...jk',u,vh)
 
-    output = []
+    output = ()
     if 'R' in requested:
-        output.append(R)
+        output+=(R,)
     if 'V' in requested:
-        output.append(_np.einsum('...ij,...kj',T,R))
+        output+=(_np.einsum('...ij,...kj',T,R),)
     if 'U' in requested:
-        output.append(_np.einsum('...ji,...jk',R,T))
+        output+=(_np.einsum('...ji,...jk',R,T),)
 
     if len(output) == 0:
         raise ValueError('output needs to be out of V, R, U')
 
-    return tuple(output)
+    return output
 
 
 def _equivalent_Mises(T_sym,s):

python/setup.py

@@ -23,7 +23,7 @@ setuptools.setup(
         'h5py>=2.9',                                                                                # requires numpy
         'vtk>=8.1',
         'matplotlib>=3.0',                                                                          # requires numpy, pillow
-        'pyaml>=3.12'
+        'pyyaml>=3.12'
     ],
     classifiers = [
         'Intended Audience :: Science/Research',

python/tests/reference/Result/compressionY.yaml

@@ -5,12 +5,12 @@ solver:
 loadstep:
   - boundary_conditions:
       mechanical:
-        dot_F: [x, 0,       0,
+        dot_F: [[x, 0,       0],
-                0, -1.0e-3, 0,
+                [0, -1.0e-3, 0],
-                0, 0,       x]
+                [0, 0,       x]]
-        P: [0, x, x,
+        P: [[0, x, x],
-            x, x, x,
+            [x, x, x],
-            x, x, 0]
+            [x, x, 0]]
     discretization:
       t: 5
       N: 10

python/tests/reference/Result/export_VTK/test_vtk[0-0-0].md5

@@ -1 +1 @@
-d5db0be324a959f00245e42704ea2d6f
+a40baead936c79dd4f86f84ad858b9fa

python/tests/reference/Result/export_VTK/test_vtk[0-0-1].md5

@@ -1 +1 @@
-fe9ddaf54ac1fb785094251d29fcdc9c
+6fb37bd65934de859dd6b6e0191e7d64

python/tests/reference/Result/export_VTK/test_vtk[0-0-2].md5

@@ -1 +1 @@
-9c8ac0bb1eb4a7b9ebc3e5fd5840b0a4
+61953c35f61f3234b98d78a912e7dc83

python/tests/reference/Result/export_VTK/test_vtk[0-0-3].md5

@@ -0,0 +1 @@
+bb783bb80ff04dd435e814f4b82a3234

python/tests/reference/Result/export_VTK/test_vtk[1-0-0].md5

@@ -1 +1 @@
-1b9ebd17c5257e2edba48d006f25d4e6
+4f85d2613aa70622a2d5f49dc8bf2eb2

python/tests/reference/Result/export_VTK/test_vtk[1-0-1].md5

@@ -1 +1 @@
-8967bb1a6c329a072baaa83da534ae56
+e1ca5306082fc3ab411f5ddab1a2e370

python/tests/reference/Result/export_VTK/test_vtk[1-0-2].md5

@@ -1 +1 @@
-752e8b6186ad2b6b1b5c781940669cb1
+1641c3b3641e942ffc325d471bdfaf00

python/tests/reference/Result/export_VTK/test_vtk[1-0-3].md5

@@ -0,0 +1 @@
+ba97286c5d95bf817143f7bb9cf58421

python/tests/reference/Result/tensionY.yaml

@@ -5,12 +5,12 @@ solver:
 loadstep:
   - boundary_conditions:
       mechanical:
-        dot_F: [x, 0,      0,
+        dot_F: [[x, 0,      0],
-                0, 1.0e-3, 0,
+                [0, 1.0e-3, 0],
-                0, 0,      x]
+                [0, 0,      x]]
-        P: [0, x, x,
+        P: [[0, x, x],
-            x, x, x,
+            [x, x, x],
-            x, x, 0]
+            [x, x, 0]]
     discretization:
       t: 20
       N: 40

python/tests/test_Crystal.py

@@ -1,10 +1,20 @@
 import pytest
 import numpy as np
 
+import damask
 from damask import Crystal
 
 class TestCrystal:
 
+    @pytest.mark.parametrize('lattice,family',[('aP','cubic'),('xI','cubic')])
+    def test_invalid_init(self,lattice,family):
+        with pytest.raises(KeyError):
+            Crystal(family=family,lattice=lattice)
+
+    def test_eq(self):
+        family = np.random.choice(list(damask._crystal.lattice_symmetries.values()))
+        assert Crystal(family=family) == Crystal(family=family)
+
     def test_double_to_lattice(self):
         c = Crystal(lattice='cF')
         with pytest.raises(KeyError):
@@ -55,3 +65,4 @@ class TestCrystal:
                     alpha=alpha,beta=beta,gamma=gamma)
         assert np.allclose(vector,
                            c.to_frame(**{keyFrame:c.to_lattice(**{keyLattice:vector})}))
+    

python/tests/test_Result.py

@@ -13,6 +13,7 @@ import numpy as np
 
 from damask import Result
 from damask import Orientation
+from damask import VTK
 from damask import tensor
 from damask import mechanics
 from damask import grid_filters
@@ -106,7 +107,8 @@ class TestResult:
         in_file   = default.place('|F_e|')
         assert np.allclose(in_memory,in_file)
 
-    @pytest.mark.parametrize('mode',['direct','function'])
+    @pytest.mark.parametrize('mode',
+        ['direct',pytest.param('function',marks=pytest.mark.xfail(sys.platform=="darwin",reason='n/a'))])
     def test_add_calculation(self,default,tmp_path,mode):
 
         if mode == 'direct':
@@ -123,6 +125,10 @@ class TestResult:
         in_file   = default.place('x')
         assert np.allclose(in_memory,in_file)
 
+    def test_add_calculation_invalid(self,default):
+        default.add_calculation('np.linalg.norm(#F#,axis=0)','wrong_dim')
+        assert default.get('wrong_dim') is None
+
     def test_add_stress_Cauchy(self,default):
         default.add_stress_Cauchy('P','F')
         in_memory = mechanics.stress_Cauchy(default.place('P'), default.place('F'))
@@ -264,10 +270,15 @@ class TestResult:
         in_file   = default.place('V(F)')
         assert np.allclose(in_memory,in_file)
 
-    def test_add_invalid(self,default):
+    def test_add_invalid_dataset(self,default):
         with pytest.raises(TypeError):
             default.add_calculation('#invalid#*2')
 
+    def test_add_generic_grid_invalid(self,ref_path):
+        result = Result(ref_path/'4grains2x4x3_compressionY.hdf5')
+        with pytest.raises(NotImplementedError):
+            result.add_curl('F')
+
 
     @pytest.mark.parametrize('shape',['vector','tensor'])
     def test_add_curl(self,default,shape):
@@ -360,25 +371,19 @@ class TestResult:
              b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F')
          assert np.allclose(a,b)
 
-    # need to wait for writing in parallel, output order might change if select more then one
+    @pytest.mark.parametrize('output',['F','*',['P'],['P','F']],ids=range(4))
-    @pytest.mark.parametrize('output',['F','*',['P']],ids=range(3))
     @pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
     @pytest.mark.parametrize('inc',[4,0],ids=range(2))
     def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc):
         result = Result(ref_path/fname).view('increments',inc)
         os.chdir(tmp_path)
-        result.export_VTK(output)
+        result.export_VTK(output,parallel=False)
         fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vti'
-        last = ''
+        v = VTK.load(tmp_path/fname)
-        for i in range(10):
+        v.set_comments('n/a')
-            if os.path.isfile(tmp_path/fname):
+        v.save(tmp_path/fname,parallel=False)
         with open(fname) as f:
             cur = hashlib.md5(f.read().encode()).hexdigest()
-                    if cur == last:
-                        break
-                    else:
-                        last = cur
-            time.sleep(.5)
         if update:
             with open((ref_path/'export_VTK'/request.node.name).with_suffix('.md5'),'w') as f:
                 f.write(cur)
@@ -403,6 +408,11 @@ class TestResult:
         os.chdir(tmp_path)
         single_phase.export_VTK(mode=mode)
 
+    def test_vtk_invalid_mode(self,single_phase):
+        with pytest.raises(ValueError):
+            single_phase.export_VTK(mode='invalid')
+
+
     def test_XDMF_datatypes(self,tmp_path,single_phase,update,ref_path):
         for shape in [('scalar',()),('vector',(3,)),('tensor',(3,3)),('matrix',(12,))]:
             for dtype in ['f4','f8','i1','i2','i4','i8','u1','u2','u4','u8']:
@@ -494,3 +504,14 @@ class TestResult:
         with bz2.BZ2File((ref_path/'place'/fname).with_suffix('.pbz2')) as f:
             ref = pickle.load(f)
             assert cur is None if ref is None else dict_equal(cur,ref)
+
+
+    @pytest.mark.parametrize('fname',['4grains2x4x3_compressionY.hdf5',
+                                      '6grains6x7x8_single_phase_tensionY.hdf5'])
+    @pytest.mark.parametrize('output',['material.yaml','*'])
+    @pytest.mark.parametrize('overwrite',[True,False])
+    def test_export_setup(self,ref_path,tmp_path,fname,output,overwrite):
+        os.chdir(tmp_path)
+        r = Result(ref_path/fname)
+        r.export_setup(output,overwrite)
+        r.export_setup(output,overwrite)

src/CMakeLists.txt

@@ -4,7 +4,7 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
     SET_SOURCE_FILES_PROPERTIES("lattice.f90" PROPERTIES COMPILE_FLAGS "-ffree-line-length-240")
 endif()
 
-file(GLOB damask-sources *.f90 *.c)
+file(GLOB damask-sources CONFIGURE_DEPENDS *.f90 *.c)
 
 # probably we should have a subfolder for MSC.Marc
 list(FILTER damask-sources EXCLUDE REGEX ".*CPFEM.f90")
@@ -14,7 +14,7 @@ list(FILTER damask-sources EXCLUDE REGEX ".*commercialFEM_fileList.*.f90")
 
 if (PROJECT_NAME STREQUAL "damask-grid")
 
-    file(GLOB grid-sources grid/*.f90)
+    file(GLOB grid-sources CONFIGURE_DEPENDS grid/*.f90)
 
     if (NOT CMAKE_BUILD_TYPE STREQUAL "SYNTAXONLY")
         add_executable(DAMASK_grid ${damask-sources} ${grid-sources})
@@ -28,7 +28,7 @@ if (PROJECT_NAME STREQUAL "damask-grid")
 
 elseif (PROJECT_NAME STREQUAL "damask-mesh")
       
-    file(GLOB mesh-sources mesh/*.f90)
+    file(GLOB mesh-sources CONFIGURE_DEPENDS mesh/*.f90)
 
     add_executable(DAMASK_mesh ${damask-sources} ${mesh-sources})
     install (TARGETS DAMASK_mesh RUNTIME DESTINATION bin)

src/DAMASK_interface.f90

@@ -102,6 +102,7 @@ subroutine DAMASK_interface_init
   print'(/,a)', ' Version: '//DAMASKVERSION
 
   print'(/,a)', ' Compiled with: '//compiler_version()
+  print'(a)',   ' Compiled on: '//CMAKE_SYSTEM
   print'(a)',   ' Compiler options: '//compiler_options()
 
   ! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md

src/prec.f90

@@ -13,7 +13,7 @@ module prec
   implicit none
   public
 
-  ! https://software.intel.com/en-us/blogs/2017/03/27/doctor-fortran-in-it-takes-all-kinds
+  ! https://stevelionel.com/drfortran/2017/03/27/doctor-fortran-in-it-takes-all-kinds
   integer,     parameter :: pReal      = IEEE_selected_real_kind(15,307)                            !< number with 15 significant digits, up to 1e+-307 (typically 64 bit)
   integer,     parameter :: pI32       = selected_int_kind(9)                                       !< number with at least up to +-1e9 (typically 32 bit)
   integer,     parameter :: pI64       = selected_int_kind(18)                                      !< number with at least up to +-1e18 (typically 64 bit)