import bz2 import pickle import time import shutil import os import sys import hashlib import fnmatch import random from datetime import datetime import pytest import vtk import h5py 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 @pytest.fixture def default(tmp_path,ref_path): """Small Result file in temp location for modification.""" fname = '12grains6x7x8_tensionY.hdf5' shutil.copy(ref_path/fname,tmp_path) return Result(tmp_path/fname).view(times=20.0) @pytest.fixture def single_phase(tmp_path,ref_path): """Single phase Result file in temp location for modification.""" fname = '6grains6x7x8_single_phase_tensionY.hdf5' shutil.copy(ref_path/fname,tmp_path) return Result(tmp_path/fname) @pytest.fixture def ref_path(ref_path_base): """Directory containing reference results.""" return ref_path_base/'Result' def dict_equal(d1, d2): for k in d1: if (k not in d2): return False else: if type(d1[k]) is dict: return dict_equal(d1[k],d2[k]) else: if not np.allclose(d1[k],d2[k]): return False return True class TestResult: def test_self_report(self,default): print(default) def test_view_all(self,default): a = default.view(increments=True).get('F') assert dict_equal(a,default.view(increments='*').get('F')) assert dict_equal(a,default.view(increments=default.increments_in_range(0,np.iinfo(int).max)).get('F')) assert dict_equal(a,default.view(times=True).get('F')) assert dict_equal(a,default.view(times='*').get('F')) assert dict_equal(a,default.view(times=default.times_in_range(0.0,np.inf)).get('F')) @pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations def test_view_none(self,default,what): n0 = default.view(**{what:False}) n1 = default.view(**{what:[]}) label = 'increments' if what == 'times' else what assert n0.get('F') is n1.get('F') is None and \ len(n0.visible[label]) == len(n1.visible[label]) == 0 @pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations def test_view_more(self,default,what): empty = default.view(**{what:False}) a = empty.view_more(**{what:'*'}).get('F') b = empty.view_more(**{what:True}).get('F') assert dict_equal(a,b) @pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations def test_view_less(self,default,what): full = default.view(**{what:True}) n0 = full.view_less(**{what:'*'}) n1 = full.view_less(**{what:True}) label = 'increments' if what == 'times' else what assert n0.get('F') is n1.get('F') is None and \ len(n0.visible[label]) == len(n1.visible[label]) == 0 def test_add_invalid(self,default): default.add_absolute('xxxx') def test_add_absolute(self,default): default.add_absolute('F_e') in_memory = np.abs(default.place('F_e')) in_file = default.place('|F_e|') assert np.allclose(in_memory,in_file) @pytest.mark.parametrize('mode', ['direct',pytest.param('function',marks=pytest.mark.xfail(sys.platform in ['darwin','win32'], reason='n/a'))]) def test_add_calculation(self,default,tmp_path,mode): if mode == 'direct': default.add_calculation('2.0*np.abs(#F#)-1.0','x','-','my notes') else: with open(tmp_path/'f.py','w') as f: f.write("import numpy as np\ndef my_func(field):\n return 2.0*np.abs(field)-1.0\n") sys.path.insert(0,str(tmp_path)) import f default.enable_user_function(f.my_func) default.add_calculation('my_func(#F#)','x','-','my notes') in_memory = 2.0*np.abs(default.place('F'))-1.0 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')) in_file = default.place('sigma') assert np.allclose(in_memory,in_file) def test_add_determinant(self,default): default.add_determinant('P') in_memory = np.linalg.det(default.place('P')) in_file = default.place('det(P)') assert np.allclose(in_memory,in_file) def test_add_deviator(self,default): default.add_deviator('P') in_memory = tensor.deviatoric(default.place('P')) in_file = default.place('s_P') assert np.allclose(in_memory,in_file) @pytest.mark.parametrize('eigenvalue,function',[('max',np.amax),('min',np.amin)]) def test_add_eigenvalue(self,default,eigenvalue,function): default.add_stress_Cauchy('P','F') default.add_eigenvalue('sigma',eigenvalue) in_memory = function(tensor.eigenvalues(default.place('sigma')),axis=1) in_file = default.place(f'lambda_{eigenvalue}(sigma)') assert np.allclose(in_memory,in_file) @pytest.mark.parametrize('eigenvalue,idx',[('max',2),('mid',1),('min',0)]) def test_add_eigenvector(self,default,eigenvalue,idx): default.add_stress_Cauchy('P','F') default.add_eigenvector('sigma',eigenvalue) in_memory = tensor.eigenvectors(default.place('sigma'))[:,idx] in_file = default.place(f'v_{eigenvalue}(sigma)') assert np.allclose(in_memory,in_file) @pytest.mark.parametrize('d',[[1,0,0],[0,1,0],[0,0,1]]) def test_add_IPF_color(self,default,d): default.add_IPF_color(d,'O') qu = default.place('O') crystal_structure = qu.dtype.metadata['lattice'] c = Orientation(rotation=qu,lattice=crystal_structure) in_memory = np.uint8(c.IPF_color(np.array(d))*255) in_file = default.place('IPFcolor_({} {} {})'.format(*d)) assert np.allclose(in_memory,in_file) def test_add_maximum_shear(self,default): default.add_stress_Cauchy('P','F') default.add_maximum_shear('sigma') in_memory = mechanics.maximum_shear(default.place('sigma')) in_file = default.place('max_shear(sigma)') assert np.allclose(in_memory,in_file) def test_add_Mises_strain(self,default): t = ['V','U'][np.random.randint(0,2)] m = np.random.random()*2.0 - 1.0 default.add_strain('F',t,m) label = f'epsilon_{t}^{m}(F)' default.add_equivalent_Mises(label) in_memory = mechanics.equivalent_strain_Mises(default.place(label)) in_file = default.place(label+'_vM') assert np.allclose(in_memory,in_file) def test_add_Mises_stress(self,default): default.add_stress_Cauchy('P','F') default.add_equivalent_Mises('sigma') in_memory = mechanics.equivalent_stress_Mises(default.place('sigma')) in_file = default.place('sigma_vM') assert np.allclose(in_memory,in_file) def test_add_Mises_invalid(self,default): default.add_stress_Cauchy('P','F') default.add_calculation('#sigma#','sigma_y',unit='y') default.add_equivalent_Mises('sigma_y') assert default.get('sigma_y_vM') is None def test_add_Mises_stress_strain(self,default): default.add_stress_Cauchy('P','F') default.add_calculation('#sigma#','sigma_y',unit='y') default.add_calculation('#sigma#','sigma_x',unit='x') default.add_equivalent_Mises('sigma_y',kind='strain') default.add_equivalent_Mises('sigma_x',kind='stress') assert not np.allclose(default.place('sigma_y_vM'),default.place('sigma_x_vM')) @pytest.mark.parametrize('ord',[1,2]) @pytest.mark.parametrize('dataset,axis',[('F',(1,2)),('xi_sl',(1,))]) def test_add_norm(self,default,ord,dataset,axis): default.add_norm(dataset,ord) in_memory = np.linalg.norm(default.place(dataset),ord=ord,axis=axis,keepdims=True) in_file = default.place(f'|{dataset}|_{ord}') assert np.allclose(in_memory,in_file) def test_add_stress_second_Piola_Kirchhoff(self,default): default.add_stress_second_Piola_Kirchhoff('P','F') in_memory = mechanics.stress_second_Piola_Kirchhoff(default.place('P'),default.place('F')) in_file = default.place('S') assert np.allclose(in_memory,in_file) @pytest.mark.parametrize('options',[{'uvw':[1,0,0],'with_symmetry':False}, {'uvw':[1,1,0],'with_symmetry':True}, {'hkl':[0,1,1],'with_symmetry':True}, {'hkl':[1,1,1],'with_symmetry':False}, ]) def test_add_pole(self,default,options): default.add_pole(**options) rot = default.place('O') in_memory = Orientation(rot,lattice=rot.dtype.metadata['lattice']).to_pole(**options) brackets = [['[[]','[]]'],'()','⟨⟩','{}'][('hkl' in options)*1+(options['with_symmetry'])*2] # escape fnmatch label = 'p^{}{} {} {}{}'.format(brackets[0], *(list(options.values())[0]), brackets[-1]) in_file = default.place(label) assert np.allclose(in_memory,in_file) def test_add_rotation(self,default): default.add_rotation('F') in_memory = mechanics.rotation(default.place('F')).as_matrix() in_file = default.place('R(F)') assert np.allclose(in_memory,in_file) def test_add_spherical(self,default): default.add_spherical('P') in_memory = tensor.spherical(default.place('P'),False) in_file = default.place('p_P') assert np.allclose(in_memory,in_file) def test_add_strain(self,default): t = ['V','U'][np.random.randint(0,2)] m = np.random.random()*2.0 - 1.0 default.add_strain('F',t,m) label = f'epsilon_{t}^{m}(F)' in_memory = mechanics.strain(default.place('F'),t,m) in_file = default.place(label) assert np.allclose(in_memory,in_file) def test_add_stretch_right(self,default): default.add_stretch_tensor('F','U') in_memory = mechanics.stretch_right(default.place('F')) in_file = default.place('U(F)') assert np.allclose(in_memory,in_file) def test_add_stretch_left(self,default): default.add_stretch_tensor('F','V') in_memory = mechanics.stretch_left(default.place('F')) in_file = default.place('V(F)') assert np.allclose(in_memory,in_file) 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): if shape == 'vector': default.add_calculation('#F#[:,:,0]','x','1','just a vector') if shape == 'tensor': default.add_calculation('#F#[:,:,:]','x','1','just a tensor') x = default.place('x') default.add_curl('x') in_file = default.place('curl(x)') in_memory = grid_filters.curl(default.size,x.reshape(tuple(default.cells)+x.shape[1:])).reshape(in_file.shape) assert (in_file == in_memory).all() @pytest.mark.parametrize('shape',['vector','tensor']) def test_add_divergence(self,default,shape): if shape == 'vector': default.add_calculation('#F#[:,:,0]','x','1','just a vector') if shape == 'tensor': default.add_calculation('#F#[:,:,:]','x','1','just a tensor') x = default.place('x') default.add_divergence('x') in_file = default.place('divergence(x)') in_memory = grid_filters.divergence(default.size,x.reshape(tuple(default.cells)+x.shape[1:])).reshape(in_file.shape) assert (in_file == in_memory).all() @pytest.mark.parametrize('shape',['scalar','pseudo_scalar','vector']) def test_add_gradient(self,default,shape): if shape == 'pseudo_scalar': default.add_calculation('#F#[:,0,0:1]','x','1','a pseudo scalar') if shape == 'scalar': default.add_calculation('#F#[:,0,0]','x','1','just a scalar') if shape == 'vector': default.add_calculation('#F#[:,:,1]','x','1','just a vector') x = default.place('x').reshape((np.product(default.cells),-1)) default.add_gradient('x') in_file = default.place('gradient(x)') in_memory = grid_filters.gradient(default.size,x.reshape(tuple(default.cells)+x.shape[1:])).reshape(in_file.shape) assert (in_file == in_memory).all() @pytest.mark.parametrize('overwrite',['off','on']) def test_add_overwrite(self,default,overwrite): last = default.view(increments=-1) last.add_stress_Cauchy() created_first = last.place('sigma').dtype.metadata['created'] created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z') last = last.view(protected=overwrite != 'on') time.sleep(2) try: last.add_calculation('#sigma#*0.0+311.','sigma','not the Cauchy stress') except ValueError: pass created_second = last.place('sigma').dtype.metadata['created'] created_second = datetime.strptime(created_second,'%Y-%m-%d %H:%M:%S%z') if overwrite == 'on': assert created_first < created_second and np.allclose(last.place('sigma'),311.) else: assert created_first == created_second and not np.allclose(last.place('sigma'),311.) @pytest.mark.parametrize('allowed',['off','on']) def test_rename(self,default,allowed): if allowed == 'on': F = default.place('F') default = default.view(protected=False) default.rename('F','new_name') assert np.all(F == default.place('new_name')) default = default.view(protected=True) with pytest.raises(PermissionError): default.rename('P','another_new_name') @pytest.mark.parametrize('allowed',['off','on']) def test_remove(self,default,allowed): if allowed == 'on': unsafe = default.view(protected=False) unsafe.remove('F') assert unsafe.get('F') is None else: with pytest.raises(PermissionError): default.remove('F') @pytest.mark.parametrize('mode',['cell','node']) def test_coordinates(self,default,mode): if mode == 'cell': a = grid_filters.coordinates0_point(default.cells,default.size,default.origin) b = default.coordinates0_point.reshape(tuple(default.cells)+(3,),order='F') elif mode == 'node': a = grid_filters.coordinates0_node(default.cells,default.size,default.origin) b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F') assert np.allclose(a,b) @pytest.mark.parametrize('output',['F','*',['P'],['P','F']],ids=range(4)) @pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1)) @pytest.mark.parametrize('inc',[4,0],ids=range(2)) @pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<9, reason='missing "Direction" attribute') 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) result.export_VTK(output,target_dir=tmp_path,parallel=False) fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vti' v = VTK.load(tmp_path/fname) v.comments = 'n/a' v.save(tmp_path/fname,parallel=False) with open(tmp_path/fname) as f: cur = hashlib.md5(f.read().encode()).hexdigest() if update: with open((ref_path/'export_VTK'/request.node.name).with_suffix('.md5'),'w') as f: f.write(cur+'\n') with open((ref_path/'export_VTK'/request.node.name).with_suffix('.md5')) as f: assert cur == f.read().strip('\n') @pytest.mark.parametrize('mode',['point','cell']) @pytest.mark.parametrize('output',[False,True]) def test_vtk_marc(self,tmp_path,ref_path,mode,output): os.chdir(tmp_path) result = Result(ref_path/'check_compile_job1.hdf5') result.export_VTK(output,mode) def test_marc_coordinates(self,ref_path): result = Result(ref_path/'check_compile_job1.hdf5').view(increments=-1) c_n = result.coordinates0_node + result.get('u_n') c_p = result.coordinates0_point + result.get('u_p') assert len(c_n) > len(c_p) @pytest.mark.parametrize('mode',['point','cell']) def test_vtk_mode(self,tmp_path,single_phase,mode): 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_vtk_custom_path(self,tmp_path,single_phase): export_dir = tmp_path/'export_dir' single_phase.export_VTK(mode='point',target_dir=export_dir,parallel=False) assert set(os.listdir(export_dir)) == set([f'{single_phase.fname.stem}_inc{i:02}.vtp' for i in range(0,40+1,4)]) def test_XDMF_datatypes(self,tmp_path,single_phase,update,ref_path): for what,shape in {'scalar':(),'vector':(3,),'tensor':(3,3),'matrix':(12,)}.items(): for dtype in ['f4','f8','i1','i2','i4','i8','u1','u2','u4','u8']: single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape},'{dtype}')",f'{what}_{dtype}') xdmf_path = tmp_path/single_phase.fname.with_suffix('.xdmf').name single_phase.export_XDMF(target_dir=tmp_path) if update: shutil.copy(xdmf_path,ref_path/xdmf_path.name) assert sorted(open(xdmf_path).read()) == sorted(open(ref_path/xdmf_path.name).read()) @pytest.mark.skipif(not (hasattr(vtk,'vtkXdmfReader') and hasattr(vtk.vtkXdmfReader(),'GetOutput')), reason='https://discourse.vtk.org/t/2450') def test_XDMF_shape(self,tmp_path,single_phase): single_phase.export_XDMF(target_dir=single_phase.fname.parent) fname = single_phase.fname.with_suffix('.xdmf') reader_xdmf = vtk.vtkXdmfReader() reader_xdmf.SetFileName(fname) reader_xdmf.Update() dim_xdmf = reader_xdmf.GetOutput().GetDimensions() bounds_xdmf = reader_xdmf.GetOutput().GetBounds() single_phase.view(increments=0).export_VTK(target_dir=single_phase.fname.parent,parallel=False) fname = single_phase.fname.with_name(single_phase.fname.stem+'_inc00.vti') reader_vti = vtk.vtkXMLImageDataReader() reader_vti.SetFileName(fname) reader_vti.Update() dim_vti = reader_vti.GetOutput().GetDimensions() bounds_vti = reader_vti.GetOutput().GetBounds() assert dim_vti == dim_xdmf and bounds_vti == bounds_xdmf def test_XDMF_invalid(self,default): with pytest.raises(TypeError): default.export_XDMF() def test_XDMF_custom_path(self,single_phase,tmp_path): os.chdir(tmp_path) single_phase.export_XDMF() assert single_phase.fname.with_suffix('.xdmf').name in os.listdir(tmp_path) export_dir = tmp_path/'export_dir' single_phase.export_XDMF(target_dir=export_dir) assert single_phase.fname.with_suffix('.xdmf').name in os.listdir(export_dir) @pytest.mark.skipif(not (hasattr(vtk,'vtkXdmfReader') and hasattr(vtk.vtkXdmfReader(),'GetOutput')), reason='https://discourse.vtk.org/t/2450') def test_XDMF_relabs_path(self,single_phase,tmp_path): def dims(xdmf): reader_xdmf = vtk.vtkXdmfReader() reader_xdmf.SetFileName(xdmf) reader_xdmf.Update() return reader_xdmf.GetOutput().GetDimensions() single_phase.export_XDMF(target_dir=tmp_path) xdmfname = single_phase.fname.with_suffix('.xdmf').name ref_dims = dims(tmp_path/xdmfname) for (d,info) in { 'A': dict(absolute_path=True, mv='..', ), 'B': dict(absolute_path=False, mv='../A', ), }.items(): sub = tmp_path/d; sub.mkdir(exist_ok=True) single_phase.export_XDMF(target_dir=sub,absolute_path=info['absolute_path']) os.replace(sub/xdmfname,sub/info['mv']/xdmfname) assert ref_dims == dims(sub/info['mv']/xdmfname) @pytest.mark.parametrize('view,output,flatten,prune', [({},['F','P','F','L_p','F_e','F_p'],True,True), ({'increments':3},'F',True,True), ({'increments':[1,8,3,4,5,6,7]},['F','P'],True,True), ({'phases':['A','B']},['F','P'],True,True), ({'phases':['A','C'],'homogenizations':False},['F','P','O'],True,True), ({'phases':False,'homogenizations':False},['F','P','O'],True,True), ({'phases':False},['Delta_V'],True,True), ({},['u_p','u_n'],False,False)], ids=list(range(8))) def test_get(self,update,request,ref_path,view,output,flatten,prune): result = Result(ref_path/'4grains2x4x3_compressionY.hdf5') for key,value in view.items(): result = result.view(**{key:value}) fname = request.node.name cur = result.get(output,flatten,prune) if update: with bz2.BZ2File((ref_path/'get'/fname).with_suffix('.pbz2'),'w') as f: pickle.dump(cur,f) with bz2.BZ2File((ref_path/'get'/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('view,output,flatten,constituents,prune', [({},['F','P','F','L_p','F_e','F_p'],True,True,None), ({'increments':3},'F',True,True,[0,1,2,3,4,5,6,7]), ({'increments':[1,8,3,4,5,6,7]},['F','P'],True,True,1), ({'phases':['A','B']},['F','P'],True,True,[1,2]), ({'phases':['A','C'],'homogenizations':False},['F','P','O'],True,True,[0,7]), ({'phases':False,'homogenizations':False},['F','P','O'],True,True,[1,2,3,4]), ({'phases':False},['Delta_V'],True,True,[1,2,4]), ({},['u_p','u_n'],False,False,None)], ids=list(range(8))) def test_place(self,update,request,ref_path,view,output,flatten,prune,constituents): result = Result(ref_path/'4grains2x4x3_compressionY.hdf5') for key,value in view.items(): result = result.view(**{key:value}) fname = request.node.name cur = result.place(output,flatten,prune,constituents) if update: with bz2.BZ2File((ref_path/'place'/fname).with_suffix('.pbz2'),'w') as f: pickle.dump(cur,f) 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_simulation_setup(self,ref_path,tmp_path,fname,output,overwrite): r = Result(ref_path/fname) r.export_simulation_setup(output,target_dir=tmp_path) with h5py.File(ref_path/fname,'r') as f_hdf5: for file in fnmatch.filter(f_hdf5['setup'].keys(),output): with open(tmp_path/file) as f: assert f_hdf5[f'setup/{file}'][()][0].decode() == f.read() r.export_simulation_setup(output,target_dir=tmp_path,overwrite=overwrite) def test_export_simulation_setup_custom_path(self,ref_path,tmp_path): src = ref_path/'4grains2x4x3_compressionY.hdf5' subdir = 'export_dir' absdir = tmp_path/subdir absdir.mkdir(exist_ok=True) r = Result(src) for t,cwd in zip([absdir,subdir,None],[tmp_path,tmp_path,absdir]): os.chdir(cwd) r.export_simulation_setup('material.yaml',target_dir=t) assert 'material.yaml' in os.listdir(absdir); (absdir/'material.yaml').unlink() def test_simulation_setup_files(self,ref_path): r = Result(ref_path/'4grains2x4x3_compressionY.hdf5') assert set(r.simulation_setup_files) == set(['4grains2x4x3.vti', 'compressionY.yaml', 'material.yaml']) @pytest.mark.parametrize('fname',['4grains2x4x3_compressionY.hdf5', '6grains6x7x8_single_phase_tensionY.hdf5']) def test_export_DADF5(self,ref_path,tmp_path,fname): r = Result(ref_path/fname) r = r.view(phases = random.sample(r.phases,1)) r = r.view(increments = random.sample(r.increments,np.random.randint(2,len(r.increments)))) r.export_DADF5(tmp_path/fname) r_exp = Result(tmp_path/fname) assert str(r.get()) == str(r_exp.get()) assert str(r.place()) == str(r_exp.place()) @pytest.mark.parametrize('fname',['4grains2x4x3_compressionY.hdf5', '6grains6x7x8_single_phase_tensionY.hdf5']) def test_export_DADF5_name_clash(self,ref_path,tmp_path,fname): r = Result(ref_path/fname) with pytest.raises(PermissionError): r.export_DADF5(r.fname)