diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index dd20c8baa..501b9e193 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -203,7 +203,6 @@ Post_OrientationConversion: stage: postprocessing script: - OrientationConversion/test.py - - OrientationConversion/test2.py except: - master - release diff --git a/VERSION b/VERSION index 7be7a7f6c..6e24519bd 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.3-2303-g2a6132b7 +v2.0.3-2364-g62f7363a diff --git a/processing/post/DADF5_postResults.py b/processing/post/DADF5_postResults.py index 70c883aeb..2230ba563 100755 --- a/processing/post/DADF5_postResults.py +++ b/processing/post/DADF5_postResults.py @@ -33,7 +33,7 @@ for filename in options.filenames: results = damask.Result(filename) if not results.structured: continue - coords = damask.grid_filters.cell_coord0(results.grid,results.size,results.origin) + coords = damask.grid_filters.cell_coord0(results.grid,results.size,results.origin).reshape(-1,3,order='F') N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1 N_digits = 5 # hack to keep test intact diff --git a/processing/post/addCompatibilityMismatch.py b/processing/post/addCompatibilityMismatch.py index 0678e78ba..59eafc077 100755 --- a/processing/post/addCompatibilityMismatch.py +++ b/processing/post/addCompatibilityMismatch.py @@ -16,8 +16,8 @@ scriptID = ' '.join([scriptName,damask.version]) def volTetrahedron(coords): """ Return the volume of the tetrahedron with given vertices or sides. - - Ifvertices are given they must be in a NumPy array with shape (4,3): the + + If vertices are given they must be in a NumPy array with shape (4,3): the position vectors of the 4 vertices in 3 dimensions; if the six sides are given, they must be an array of length 6. If both are given, the sides will be used in the calculation. @@ -62,19 +62,18 @@ def volTetrahedron(coords): def volumeMismatch(size,F,nodes): """ Calculates the volume mismatch. - - volume mismatch is defined as the difference between volume of reconstructed + + volume mismatch is defined as the difference between volume of reconstructed (compatible) cube and determinant of deformation gradient at Fourier point. """ coords = np.empty([8,3]) - vMismatch = np.empty(grid[::-1]) - volInitial = size.prod()/grid.prod() - + vMismatch = np.empty(F.shape[:3]) + #-------------------------------------------------------------------------------------------------- # calculate actual volume and volume resulting from deformation gradient - for k in range(grid[2]): + for k in range(grid[0]): for j in range(grid[1]): - for i in range(grid[0]): + for i in range(grid[2]): coords[0,0:3] = nodes[k, j, i ,0:3] coords[1,0:3] = nodes[k ,j, i+1,0:3] coords[2,0:3] = nodes[k ,j+1,i+1,0:3] @@ -91,47 +90,45 @@ def volumeMismatch(size,F,nodes): + abs(volTetrahedron([coords[6,0:3],coords[4,0:3],coords[1,0:3],coords[5,0:3]])) \ + abs(volTetrahedron([coords[6,0:3],coords[4,0:3],coords[1,0:3],coords[0,0:3]]))) \ /np.linalg.det(F[k,j,i,0:3,0:3]) - return vMismatch/volInitial - + return vMismatch/(size.prod()/grid.prod()) def shapeMismatch(size,F,nodes,centres): """ Routine to calculate the shape mismatch. - + shape mismatch is defined as difference between the vectors from the central point to the corners of reconstructed (combatible) volume element and the vectors calculated by deforming the initial volume element with the current deformation gradient. """ - coordsInitial = np.empty([8,3]) - sMismatch = np.empty(grid[::-1]) - + sMismatch = np.empty(F.shape[:3]) + #-------------------------------------------------------------------------------------------------- # initial positions - coordsInitial[0,0:3] = [-size[0]/grid[0],-size[1]/grid[1],-size[2]/grid[2]] - coordsInitial[1,0:3] = [+size[0]/grid[0],-size[1]/grid[1],-size[2]/grid[2]] - coordsInitial[2,0:3] = [+size[0]/grid[0],+size[1]/grid[1],-size[2]/grid[2]] - coordsInitial[3,0:3] = [-size[0]/grid[0],+size[1]/grid[1],-size[2]/grid[2]] - coordsInitial[4,0:3] = [-size[0]/grid[0],-size[1]/grid[1],+size[2]/grid[2]] - coordsInitial[5,0:3] = [+size[0]/grid[0],-size[1]/grid[1],+size[2]/grid[2]] - coordsInitial[6,0:3] = [+size[0]/grid[0],+size[1]/grid[1],+size[2]/grid[2]] - coordsInitial[7,0:3] = [-size[0]/grid[0],+size[1]/grid[1],+size[2]/grid[2]] - coordsInitial = coordsInitial/2.0 - + delta = size/grid*.5 + coordsInitial = np.vstack((delta * np.array((-1,-1,-1)), + delta * np.array((+1,-1,-1)), + delta * np.array((+1,+1,-1)), + delta * np.array((-1,+1,-1)), + delta * np.array((-1,-1,+1)), + delta * np.array((+1,-1,+1)), + delta * np.array((+1,+1,+1)), + delta * np.array((-1,+1,+1)))) + #-------------------------------------------------------------------------------------------------- # compare deformed original and deformed positions to actual positions - for k in range(grid[2]): + for k in range(grid[0]): for j in range(grid[1]): - for i in range(grid[0]): + for i in range(grid[2]): sMismatch[k,j,i] = \ + np.linalg.norm(nodes[k, j, i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[0,0:3]))\ - + np.linalg.norm(nodes[k, j, i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[1,0:3]))\ - + np.linalg.norm(nodes[k, j+1,i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[2,0:3]))\ + + np.linalg.norm(nodes[k+1,j, i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[1,0:3]))\ + + np.linalg.norm(nodes[k+1,j+1,i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[2,0:3]))\ + np.linalg.norm(nodes[k, j+1,i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[3,0:3]))\ - + np.linalg.norm(nodes[k+1,j, i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[4,0:3]))\ + + np.linalg.norm(nodes[k, j, i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[4,0:3]))\ + np.linalg.norm(nodes[k+1,j, i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[5,0:3]))\ + np.linalg.norm(nodes[k+1,j+1,i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[6,0:3]))\ - + np.linalg.norm(nodes[k+1,j+1,i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[7,0:3])) + + np.linalg.norm(nodes[k ,j+1,i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[7,0:3])) return sMismatch @@ -174,24 +171,24 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - + table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name) grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos)) - F = table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3) + F = table.get(options.defgrad).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3)) nodes = damask.grid_filters.node_coord(size,F) - + if options.shape: centers = damask.grid_filters.cell_coord(size,F) - shapeMismatch = shapeMismatch( size,table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3),nodes,centers) + shapeMismatch = shapeMismatch(size,F,nodes,centers) table.add('shapeMismatch(({}))'.format(options.defgrad), - shapeMismatch.reshape(-1,1), + shapeMismatch.reshape(-1,1,order='F'), scriptID+' '+' '.join(sys.argv[1:])) - + if options.volume: - volumeMismatch = volumeMismatch(size,table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3),nodes) + volumeMismatch = volumeMismatch(size,F,nodes) table.add('volMismatch(({}))'.format(options.defgrad), - volumeMismatch.reshape(-1,1), + volumeMismatch.reshape(-1,1,order='F'), scriptID+' '+' '.join(sys.argv[1:])) table.to_ASCII(sys.stdout if name is None else name) diff --git a/processing/post/addCurl.py b/processing/post/addCurl.py index 87d1ab2f6..17459a2df 100755 --- a/processing/post/addCurl.py +++ b/processing/post/addCurl.py @@ -49,9 +49,10 @@ for name in filenames: for label in options.labels: field = table.get(label) shape = (3,) if np.prod(field.shape)//np.prod(grid) == 3 else (3,3) # vector or tensor - field = field.reshape(np.append(grid[::-1],shape)) + field = field.reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+shape) + curl = damask.grid_filters.curl(size,field) table.add('curlFFT({})'.format(label), - damask.grid_filters.curl(size[::-1],field).reshape(-1,np.prod(shape)), + curl.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape),order='F'), scriptID+' '+' '.join(sys.argv[1:])) - + table.to_ASCII(sys.stdout if name is None else name) diff --git a/processing/post/addDisplacement.py b/processing/post/addDisplacement.py index f74d876bc..6f4a60192 100755 --- a/processing/post/addDisplacement.py +++ b/processing/post/addDisplacement.py @@ -5,8 +5,6 @@ import sys from io import StringIO from optparse import OptionParser -import numpy as np - import damask @@ -51,23 +49,23 @@ for name in filenames: table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name) grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos)) - - F = table.get(options.f).reshape(np.append(grid[::-1],(3,3))) + + F = table.get(options.f).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3)) if options.nodal: - table = damask.Table(damask.grid_filters.node_coord0(grid[::-1],size[::-1]).reshape(-1,3), + table = damask.Table(damask.grid_filters.node_coord0(grid,size).reshape(-1,3,order='F'), {'pos':(3,)}) table.add('avg({}).{}'.format(options.f,options.pos), - damask.grid_filters.node_displacement_avg(size[::-1],F).reshape(-1,3), + damask.grid_filters.node_displacement_avg(size,F).reshape(-1,3,order='F'), scriptID+' '+' '.join(sys.argv[1:])) table.add('fluct({}).{}'.format(options.f,options.pos), - damask.grid_filters.node_displacement_fluct(size[::-1],F).reshape(-1,3), + damask.grid_filters.node_displacement_fluct(size,F).reshape(-1,3,order='F'), scriptID+' '+' '.join(sys.argv[1:])) table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt') else: table.add('avg({}).{}'.format(options.f,options.pos), - damask.grid_filters.cell_displacement_avg(size[::-1],F).reshape(-1,3), + damask.grid_filters.cell_displacement_avg(size,F).reshape(-1,3,order='F'), scriptID+' '+' '.join(sys.argv[1:])) table.add('fluct({}).{}'.format(options.f,options.pos), - damask.grid_filters.cell_displacement_fluct(size[::-1],F).reshape(-1,3), + damask.grid_filters.cell_displacement_fluct(size,F).reshape(-1,3,order='F'), scriptID+' '+' '.join(sys.argv[1:])) table.to_ASCII(sys.stdout if name is None else name) diff --git a/processing/post/addDivergence.py b/processing/post/addDivergence.py index 2619bc499..50048b44e 100755 --- a/processing/post/addDivergence.py +++ b/processing/post/addDivergence.py @@ -49,9 +49,10 @@ for name in filenames: for label in options.labels: field = table.get(label) shape = (3,) if np.prod(field.shape)//np.prod(grid) == 3 else (3,3) # vector or tensor - field = field.reshape(np.append(grid[::-1],shape)) + field = field.reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+shape) + div = damask.grid_filters.divergence(size,field) table.add('divFFT({})'.format(label), - damask.grid_filters.divergence(size[::-1],field).reshape(-1,np.prod(shape)//3), + div.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)//3,order='F'), scriptID+' '+' '.join(sys.argv[1:])) - + table.to_ASCII(sys.stdout if name is None else name) diff --git a/processing/post/addGradient.py b/processing/post/addGradient.py index 409b2ce6d..f63f24789 100755 --- a/processing/post/addGradient.py +++ b/processing/post/addGradient.py @@ -49,9 +49,10 @@ for name in filenames: for label in options.labels: field = table.get(label) shape = (1,) if np.prod(field.shape)//np.prod(grid) == 1 else (3,) # scalar or vector - field = field.reshape(np.append(grid[::-1],shape)) + field = field.reshape(tuple(grid)+(-1,),order='F') + grad = damask.grid_filters.gradient(size,field) table.add('gradFFT({})'.format(label), - damask.grid_filters.gradient(size[::-1],field).reshape(-1,np.prod(shape)*3), + grad.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)*3,order='F'), scriptID+' '+' '.join(sys.argv[1:])) - + table.to_ASCII(sys.stdout if name is None else name) diff --git a/processing/post/averageDown.py b/processing/post/averageDown.py index 39d925d19..341cc748d 100755 --- a/processing/post/averageDown.py +++ b/processing/post/averageDown.py @@ -61,7 +61,7 @@ if any(shift != 0): prefix += 'shift{:+}{:+}{:+}_'.format(*shift) for name in filenames: damask.util.report(scriptName,name) - + table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name) if (options.grid is None or options.size is None): @@ -87,11 +87,11 @@ for name in filenames: origin = list(-(packing//2)) + [0])\ [::packing[0],::packing[1],::packing[2],:].reshape((packedGrid.prod(),-1),order = 'F') - + table = damask.Table(averagedDown,table.shapes,table.comments) coords = damask.grid_filters.cell_coord0(packedGrid,size,shift/packedGrid*size+origin) - table.set(options.pos, coords.reshape(-1,3)) + table.set(options.pos, coords.reshape(-1,3,order='F')) outname = os.path.join(os.path.dirname(name),prefix+os.path.basename(name)) diff --git a/processing/post/blowUp.py b/processing/post/blowUp.py index 316b74753..23c6b2ef2 100755 --- a/processing/post/blowUp.py +++ b/processing/post/blowUp.py @@ -59,13 +59,13 @@ for name in filenames: packing = np.array(options.packing,'i') outSize = grid*packing - data = table.data.values.reshape(tuple(grid)+(-1,)) - blownUp = ndimage.interpolation.zoom(data,tuple(packing)+(1,),order=0,mode='nearest').reshape(outSize.prod(),-1) + data = table.data.values.reshape(tuple(grid)+(-1,),order='F') + blownUp = ndimage.interpolation.zoom(data,tuple(packing)+(1,),order=0,mode='nearest').reshape(outSize.prod(),-1,order='F') table = damask.Table(blownUp,table.shapes,table.comments) coords = damask.grid_filters.cell_coord0(outSize,size,origin) - table.set(options.pos,coords.reshape(-1,3)) + table.set(options.pos,coords.reshape(-1,3,order='F')) table.set('elem',np.arange(1,outSize.prod()+1)) outname = os.path.join(os.path.dirname(name),prefix+os.path.basename(name)) diff --git a/processing/post/permuteData.py b/processing/post/permuteData.py index 81af71adb..72759f2ce 100755 --- a/processing/post/permuteData.py +++ b/processing/post/permuteData.py @@ -60,7 +60,7 @@ for name in filenames: table.head_read() -# ------------------------------------------ process labels --------------------------------------- +# ------------------------------------------ process labels --------------------------------------- errors = [] remarks = [] @@ -80,7 +80,7 @@ for name in filenames: damask.util.croak(errors) table.close(dismiss = True) continue - + # ------------------------------------------ assemble header --------------------------------------- randomSeed = int(os.urandom(4).hex(), 16) if options.randomSeed is None else options.randomSeed # random seed per file @@ -97,17 +97,17 @@ for name in filenames: for col,dim in zip(columns,dims): if options.unique: s = set(map(tuple,table.data[:,col:col+dim])) # generate set of (unique) values - uniques = np.array(map(np.array,s)) # translate set to np.array + uniques = np.array(list(map(np.array,s))) # translate set to np.array shuffler = dict(zip(s,np.random.permutation(len(s)))) # random permutation - table.data[:,col:col+dim] = uniques[np.array(map(lambda x: shuffler[tuple(x)], - table.data[:,col:col+dim]))] # fill table with mapped uniques + table.data[:,col:col+dim] = uniques[np.array(list(map(lambda x: shuffler[tuple(x)], + table.data[:,col:col+dim])))] # fill table with mapped uniques else: np.random.shuffle(table.data[:,col:col+dim]) # independently shuffle every row -# ------------------------------------------ output result ----------------------------------------- +# ------------------------------------------ output result ----------------------------------------- table.data_writeArray() -# ------------------------------------------ output finalization ----------------------------------- +# ------------------------------------------ output finalization ----------------------------------- table.close() # close ASCII tables diff --git a/processing/pre/geom_fromVoronoiTessellation.py b/processing/pre/geom_fromVoronoiTessellation.py index df40176d8..e6755c28e 100755 --- a/processing/pre/geom_fromVoronoiTessellation.py +++ b/processing/pre/geom_fromVoronoiTessellation.py @@ -24,22 +24,22 @@ def findClosestSeed(seeds, weights, point): def Laguerre_tessellation(grid, size, seeds, weights, origin = np.zeros(3), periodic = True, cpus = 2): if periodic: - weights_p = np.tile(weights,27).flatten(order='F') # Laguerre weights (1,2,3,1,2,3,...,1,2,3) + weights_p = np.tile(weights.squeeze(),27) # Laguerre weights (1,2,3,1,2,3,...,1,2,3) seeds_p = np.vstack((seeds -np.array([size[0],0.,0.]),seeds, seeds +np.array([size[0],0.,0.]))) seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.]))) seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]]))) - coords = damask.grid_filters.cell_coord0(grid*3,size*3,-origin-size).reshape(-1,3,order='F') + coords = damask.grid_filters.cell_coord0(grid*3,size*3,-origin-size).reshape(-1,3) else: - weights_p = weights.flatten() + weights_p = weights.squeeze() seeds_p = seeds - coords = damask.grid_filters.cell_coord0(grid,size,-origin).reshape(-1,3,order='F') + coords = damask.grid_filters.cell_coord0(grid,size,-origin).reshape(-1,3) if cpus > 1: pool = multiprocessing.Pool(processes = cpus) result = pool.map_async(partial(findClosestSeed,seeds_p,weights_p), [coord for coord in coords]) pool.close() pool.join() - closest_seed = np.array(result.get()) + closest_seed = np.array(result.get()).reshape(-1,3) else: closest_seed= np.array([findClosestSeed(seeds_p,weights_p,coord) for coord in coords]) @@ -52,7 +52,7 @@ def Laguerre_tessellation(grid, size, seeds, weights, origin = np.zeros(3), peri def Voronoi_tessellation(grid, size, seeds, origin = np.zeros(3), periodic = True): - coords = damask.grid_filters.cell_coord0(grid,size,-origin).reshape(-1,3,order='F') + coords = damask.grid_filters.cell_coord0(grid,size,-origin).reshape(-1,3) KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds) devNull,closest_seed = KDTree.query(coords) diff --git a/processing/pre/seeds_fromGeom.py b/processing/pre/seeds_fromGeom.py index 80dc0d6f5..0b741a077 100755 --- a/processing/pre/seeds_fromGeom.py +++ b/processing/pre/seeds_fromGeom.py @@ -45,7 +45,7 @@ options.blacklist = [int(i) for i in options.blacklist] for name in filenames: damask.util.report(scriptName,name) - + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) microstructure = geom.get_microstructure().reshape((-1,1),order='F') @@ -53,9 +53,9 @@ for name in filenames: np.full(geom.grid.prod(),True,dtype=bool), np.in1d(microstructure,options.blacklist,invert=True) if options.blacklist else \ np.full(geom.grid.prod(),True,dtype=bool)) - - seeds = damask.grid_filters.cell_coord0(geom.grid,geom.size).reshape(-1,3) - + + seeds = damask.grid_filters.cell_coord0(geom.grid,geom.size).reshape(-1,3,order='F') + comments = geom.comments \ + [scriptID + ' ' + ' '.join(sys.argv[1:]), 'grid\ta {}\tb {}\tc {}'.format(*geom.grid), diff --git a/processing/pre/seeds_fromRandom.py b/processing/pre/seeds_fromRandom.py index 2de513c2c..be690713c 100755 --- a/processing/pre/seeds_fromRandom.py +++ b/processing/pre/seeds_fromRandom.py @@ -128,7 +128,7 @@ for name in filenames: if not options.selective: - coords = damask.grid_filters.cell_coord0(grid,size).reshape(-1,3) + coords = damask.grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F') seeds = coords[np.random.choice(np.prod(grid), options.N, replace=False)] \ + np.broadcast_to(size/grid,(options.N,3))*(np.random.rand(options.N,3)*.5-.25) # wobble without leaving grid else: diff --git a/python/damask/_geom.py b/python/damask/_geom.py index e2c2428fe..892000b7c 100644 --- a/python/damask/_geom.py +++ b/python/damask/_geom.py @@ -322,11 +322,10 @@ class Geom: if i != grid.prod(): raise TypeError('Invalid file: expected {} entries, found {}'.format(grid.prod(),i)) - microstructure = microstructure.reshape(grid,order='F') - if not np.any(np.mod(microstructure.flatten(),1) != 0.0): # no float present + if not np.any(np.mod(microstructure,1) != 0.0): # no float present microstructure = microstructure.astype('int') - return Geom(microstructure.reshape(grid),size,origin,homogenization,comments) + return Geom(microstructure.reshape(grid,order='F'),size,origin,homogenization,comments) @staticmethod @@ -352,16 +351,15 @@ class Geom: """ if periodic: - weights_p = np.tile(weights,27).flatten(order='F') # Laguerre weights (1,2,3,1,2,3,...,1,2,3) + weights_p = np.tile(weights,27) # Laguerre weights (1,2,3,1,2,3,...,1,2,3) seeds_p = np.vstack((seeds -np.array([size[0],0.,0.]),seeds, seeds +np.array([size[0],0.,0.]))) seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.]))) seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]]))) - coords = grid_filters.cell_coord0(grid*3,size*3,-size).reshape(-1,3,order='F') - + coords = grid_filters.cell_coord0(grid*3,size*3,-size).reshape(-1,3) else: - weights_p = weights.flatten() + weights_p = weights seeds_p = seeds - coords = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F') + coords = grid_filters.cell_coord0(grid,size).reshape(-1,3) pool = multiprocessing.Pool(processes = int(Environment().options['DAMASK_NUM_THREADS'])) result = pool.map_async(partial(Geom._find_closest_seed,seeds_p,weights_p), [coord for coord in coords]) @@ -396,7 +394,7 @@ class Geom: perform a periodic tessellation. Defaults to True. """ - coords = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F') + coords = grid_filters.cell_coord0(grid,size).reshape(-1,3) KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds) devNull,microstructure = KDTree.query(coords) diff --git a/python/damask/_result.py b/python/damask/_result.py index ee7d696a9..b2f599176 100644 --- a/python/damask/_result.py +++ b/python/damask/_result.py @@ -68,12 +68,12 @@ class Result: self.con_physics = [] for c in self.constituents: self.con_physics += f['/'.join([self.increments[0],'constituent',c])].keys() - self.con_physics = list(set(self.con_physics)) # make unique + self.con_physics = list(set(self.con_physics)) # make unique self.mat_physics = [] for m in self.materialpoints: self.mat_physics += f['/'.join([self.increments[0],'materialpoint',m])].keys() - self.mat_physics = list(set(self.mat_physics)) # make unique + self.mat_physics = list(set(self.mat_physics)) # make unique self.selection = {'increments': self.increments, 'constituents': self.constituents,'materialpoints': self.materialpoints, @@ -86,13 +86,19 @@ class Result: def __repr__(self): """Show selected data.""" all_selected_increments = self.selection['increments'] + self.pick('increments',all_selected_increments[0:1]) first = self.list_data() + self.pick('increments',all_selected_increments[-1:]) - last = self.list_data() + last = '' if len(all_selected_increments) < 2 else self.list_data() + self.pick('increments',all_selected_increments) - in_between = ''.join(['\n{}\n ...\n'.format(inc) for inc in all_selected_increments[1:-2]]) - return util.srepr(first+ in_between + last) + + in_between = '' if len(all_selected_increments) < 3 else \ + ''.join(['\n{}\n ...\n'.format(inc) for inc in all_selected_increments[1:-2]]) + + return util.srepr(first + in_between + last) def _manage_selection(self,action,what,datasets): @@ -105,7 +111,7 @@ class Result: select from 'set', 'add', and 'del' what : str attribute to change (must be from self.selection) - datasets : list of str or Boolean + datasets : list of str or bool name of datasets as list, supports ? and * wildcards. True is equivalent to [*], False is equivalent to [] @@ -197,7 +203,7 @@ class Result: ---------- what : str attribute to change (must be from self.selection) - datasets : list of str or Boolean + datasets : list of str or bool name of datasets as list, supports ? and * wildcards. True is equivalent to [*], False is equivalent to [] @@ -213,7 +219,7 @@ class Result: ---------- what : str attribute to change (must be from self.selection) - datasets : list of str or Boolean + datasets : list of str or bool name of datasets as list, supports ? and * wildcards. True is equivalent to [*], False is equivalent to [] @@ -229,7 +235,7 @@ class Result: ---------- what : str attribute to change (must be from self.selection) - datasets : list of str or Boolean + datasets : list of str or bool name of datasets as list, supports ? and * wildcards. True is equivalent to [*], False is equivalent to [] @@ -256,10 +262,10 @@ class Result: datasets : iterable or str component : int homogenization component to consider for constituent data - tagged : Boolean + tagged : bool tag Table.column name with '#component' defaults to False - split : Boolean + split : bool split Table by increment and return dictionary of Tables defaults to True @@ -320,7 +326,7 @@ class Result: Parameters ---------- - datasets : iterable or str or Boolean + datasets : iterable or str or bool Examples -------- @@ -454,7 +460,7 @@ class Result: def cell_coordinates(self): """Return initial coordinates of the cell centers.""" if self.structured: - return grid_filters.cell_coord0(self.grid,self.size,self.origin).reshape(-1,3) + return grid_filters.cell_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F') else: with h5py.File(self.fname,'r') as f: return f['geometry/x_c'][()] @@ -1009,7 +1015,7 @@ class Result: continue lock.acquire() with h5py.File(self.fname, 'a') as f: - try: + try: # ToDo: Replace if exists? dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data']) for l,v in result[1]['meta'].items(): dataset.attrs[l]=v.encode() diff --git a/python/damask/grid_filters.py b/python/damask/grid_filters.py index 8106ed905..eaee42924 100644 --- a/python/damask/grid_filters.py +++ b/python/damask/grid_filters.py @@ -1,3 +1,17 @@ +""" +Filters for operations on regular grids. + +Notes +----- +The grids are defined as (x,y,z,...) where x is fastest and z is slowest. +This convention is consistent with the geom file format. +When converting to/from a plain list (e.g. storage in ASCII table), +the following operations are required for tensorial data: + +D3 = D1.reshape(grid+(-1,),order='F').reshape(grid+(3,3)) +D1 = D3.reshape(grid+(-1,)).reshape(-1,9,order='F') + +""" from scipy import spatial as _spatial import numpy as _np @@ -7,8 +21,12 @@ def _ks(size,grid,first_order=False): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. + grid : numpy.ndarray of shape (3) + number of grid points. + first_order : bool, optional + correction for first order derivatives, defaults to False. """ k_sk = _np.where(_np.arange(grid[0])>grid[0]//2,_np.arange(grid[0])-grid[0],_np.arange(grid[0]))/size[0] @@ -19,8 +37,7 @@ def _ks(size,grid,first_order=False): k_si = _np.arange(grid[2]//2+1)/size[2] - kk, kj, ki = _np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij') - return _np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3) + return _np.stack(_np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij'), axis=-1) def curl(size,field): @@ -29,8 +46,10 @@ def curl(size,field): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. + field : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3) + periodic field of which the curl is calculated. """ n = _np.prod(field.shape[3:]) @@ -41,8 +60,8 @@ def curl(size,field): e[0, 2, 1] = e[2, 1, 0] = e[1, 0, 2] = -1.0 field_fourier = _np.fft.rfftn(field,axes=(0,1,2)) - curl_ = (_np.einsum('slm,ijkl,ijkm ->ijks', e,k_s,field_fourier)*2.0j*_np.pi if n == 3 else # vector, 3 -> 3 - _np.einsum('slm,ijkl,ijknm->ijksn',e,k_s,field_fourier)*2.0j*_np.pi) # tensor, 3x3 -> 3x3 + curl_ = (_np.einsum('slm,ijkl,ijkm ->ijks', e,k_s,field_fourier)*2.0j*_np.pi if n == 3 else # vector, 3 -> 3 + _np.einsum('slm,ijkl,ijknm->ijksn',e,k_s,field_fourier)*2.0j*_np.pi) # tensor, 3x3 -> 3x3 return _np.fft.irfftn(curl_,axes=(0,1,2),s=field.shape[:3]) @@ -53,36 +72,40 @@ def divergence(size,field): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. + field : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3) + periodic field of which the divergence is calculated. """ n = _np.prod(field.shape[3:]) k_s = _ks(size,field.shape[:3],True) field_fourier = _np.fft.rfftn(field,axes=(0,1,2)) - div_ = (_np.einsum('ijkl,ijkl ->ijk', k_s,field_fourier)*2.0j*_np.pi if n == 3 else # vector, 3 -> 1 - _np.einsum('ijkm,ijklm->ijkl',k_s,field_fourier)*2.0j*_np.pi) # tensor, 3x3 -> 3 + div_ = (_np.einsum('ijkl,ijkl ->ijk', k_s,field_fourier)*2.0j*_np.pi if n == 3 else # vector, 3 -> 1 + _np.einsum('ijkm,ijklm->ijkl',k_s,field_fourier)*2.0j*_np.pi) # tensor, 3x3 -> 3 return _np.fft.irfftn(div_,axes=(0,1,2),s=field.shape[:3]) def gradient(size,field): """ - Calculate gradient of a vector or scalar field in Fourier space. + Calculate gradient of a scalar or vector field in Fourier space. Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. + field : numpy.ndarray of shape (:,:,:,1) or (:,:,:,3) + periodic field of which the gradient is calculated. """ n = _np.prod(field.shape[3:]) k_s = _ks(size,field.shape[:3],True) field_fourier = _np.fft.rfftn(field,axes=(0,1,2)) - grad_ = (_np.einsum('ijkl,ijkm->ijkm', field_fourier,k_s)*2.0j*_np.pi if n == 1 else # scalar, 1 -> 3 - _np.einsum('ijkl,ijkm->ijklm',field_fourier,k_s)*2.0j*_np.pi) # vector, 3 -> 3x3 + grad_ = (_np.einsum('ijkl,ijkm->ijkm', field_fourier,k_s)*2.0j*_np.pi if n == 1 else # scalar, 1 -> 3 + _np.einsum('ijkl,ijkm->ijklm',field_fourier,k_s)*2.0j*_np.pi) # vector, 3 -> 3x3 return _np.fft.irfftn(grad_,axes=(0,1,2),s=field.shape[:3]) @@ -93,9 +116,9 @@ def cell_coord0(grid,size,origin=_np.zeros(3)): Parameters ---------- - grid : numpy.ndarray + grid : numpy.ndarray of shape (3) number of grid points. - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. origin : numpy.ndarray, optional physical origin of the periodic field. Defaults to [0.0,0.0,0.0]. @@ -103,7 +126,11 @@ def cell_coord0(grid,size,origin=_np.zeros(3)): """ start = origin + size/grid*.5 end = origin + size - size/grid*.5 - return _np.mgrid[start[0]:end[0]:grid[0]*1j,start[1]:end[1]:grid[1]*1j,start[2]:end[2]:grid[2]*1j].T + + return _np.stack(_np.meshgrid(_np.linspace(start[0],end[0],grid[0]), + _np.linspace(start[1],end[1],grid[1]), + _np.linspace(start[2],end[2],grid[2]),indexing = 'ij'), + axis = -1) def cell_displacement_fluct(size,F): @@ -112,7 +139,7 @@ def cell_displacement_fluct(size,F): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. F : numpy.ndarray deformation gradient field. @@ -139,14 +166,14 @@ def cell_displacement_avg(size,F): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. F : numpy.ndarray deformation gradient field. """ F_avg = _np.average(F,axis=(0,1,2)) - return _np.einsum('ml,ijkl->ijkm',F_avg-_np.eye(3),cell_coord0(F.shape[:3][::-1],size)) + return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),cell_coord0(F.shape[:3],size)) def cell_displacement(size,F): @@ -155,7 +182,7 @@ def cell_displacement(size,F): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. F : numpy.ndarray deformation gradient field. @@ -170,25 +197,25 @@ def cell_coord(size,F,origin=_np.zeros(3)): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. F : numpy.ndarray deformation gradient field. - origin : numpy.ndarray, optional + origin : numpy.ndarray of shape (3), optional physical origin of the periodic field. Defaults to [0.0,0.0,0.0]. """ - return cell_coord0(F.shape[:3][::-1],size,origin) + cell_displacement(size,F) + return cell_coord0(F.shape[:3],size,origin) + cell_displacement(size,F) def cell_coord0_gridSizeOrigin(coord0,ordered=True): """ - Return grid 'DNA', i.e. grid, size, and origin from array of cell positions. + Return grid 'DNA', i.e. grid, size, and origin from 1D array of cell positions. Parameters ---------- - coord0 : numpy.ndarray - array of undeformed cell coordinates. + coord0 : numpy.ndarray of shape (:,3) + undeformed cell coordinates. ordered : bool, optional expect coord0 data to be ordered (x fast, z slow). @@ -211,13 +238,13 @@ def cell_coord0_gridSizeOrigin(coord0,ordered=True): start = origin + delta*.5 end = origin - delta*.5 + size - if not _np.allclose(coords[0],_np.linspace(start[0],end[0],grid[0])) and \ - _np.allclose(coords[1],_np.linspace(start[1],end[1],grid[1])) and \ - _np.allclose(coords[2],_np.linspace(start[2],end[2],grid[2])): + if not (_np.allclose(coords[0],_np.linspace(start[0],end[0],grid[0])) and \ + _np.allclose(coords[1],_np.linspace(start[1],end[1],grid[1])) and \ + _np.allclose(coords[2],_np.linspace(start[2],end[2],grid[2]))): raise ValueError('Regular grid spacing violated.') - if ordered and not _np.allclose(coord0.reshape(tuple(grid[::-1])+(3,)),cell_coord0(grid,size,origin)): - raise ValueError('I_nput data is not a regular grid.') + if ordered and not _np.allclose(coord0.reshape(tuple(grid)+(3,),order='F'),cell_coord0(grid,size,origin)): + raise ValueError('Input data is not ordered (x fast, z slow).') return (grid,size,origin) @@ -241,17 +268,18 @@ def node_coord0(grid,size,origin=_np.zeros(3)): Parameters ---------- - grid : numpy.ndarray + grid : numpy.ndarray of shape (3) number of grid points. - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. - origin : numpy.ndarray, optional + origin : numpy.ndarray of shape (3), optional physical origin of the periodic field. Defaults to [0.0,0.0,0.0]. """ - return _np.mgrid[origin[0]:size[0]+origin[0]:(grid[0]+1)*1j, - origin[1]:size[1]+origin[1]:(grid[1]+1)*1j, - origin[2]:size[2]+origin[2]:(grid[2]+1)*1j].T + return _np.stack(_np.meshgrid(_np.linspace(origin[0],size[0]+origin[0],grid[0]+1), + _np.linspace(origin[1],size[1]+origin[1],grid[1]+1), + _np.linspace(origin[2],size[2]+origin[2],grid[2]+1),indexing = 'ij'), + axis = -1) def node_displacement_fluct(size,F): @@ -260,7 +288,7 @@ def node_displacement_fluct(size,F): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. F : numpy.ndarray deformation gradient field. @@ -275,14 +303,14 @@ def node_displacement_avg(size,F): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. F : numpy.ndarray deformation gradient field. """ F_avg = _np.average(F,axis=(0,1,2)) - return _np.einsum('ml,ijkl->ijkm',F_avg-_np.eye(3),node_coord0(F.shape[:3][::-1],size)) + return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),node_coord0(F.shape[:3],size)) def node_displacement(size,F): @@ -291,7 +319,7 @@ def node_displacement(size,F): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. F : numpy.ndarray deformation gradient field. @@ -306,15 +334,15 @@ def node_coord(size,F,origin=_np.zeros(3)): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size of the periodic field. F : numpy.ndarray deformation gradient field. - origin : numpy.ndarray, optional + origin : numpy.ndarray of shape (3), optional physical origin of the periodic field. Defaults to [0.0,0.0,0.0]. """ - return node_coord0(F.shape[:3][::-1],size,origin) + node_displacement(size,F) + return node_coord0(F.shape[:3],size,origin) + node_displacement(size,F) def cell_2_node(cell_data): @@ -335,14 +363,14 @@ def node_2_cell(node_data): return c[:-1,:-1,:-1] -def node_coord0_gridSizeOrigin(coord0,ordered=False): +def node_coord0_gridSizeOrigin(coord0,ordered=True): """ - Return grid 'DNA', i.e. grid, size, and origin from array of nodal positions. + Return grid 'DNA', i.e. grid, size, and origin from 1D array of nodal positions. Parameters ---------- - coord0 : numpy.ndarray - array of undeformed nodal coordinates. + coord0 : numpy.ndarray of shape (:,3) + undeformed nodal coordinates. ordered : bool, optional expect coord0 data to be ordered (x fast, z slow). @@ -357,13 +385,13 @@ def node_coord0_gridSizeOrigin(coord0,ordered=False): if (grid+1).prod() != len(coord0): raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid)) - if not _np.allclose(coords[0],_np.linspace(mincorner[0],maxcorner[0],grid[0]+1)) and \ - _np.allclose(coords[1],_np.linspace(mincorner[1],maxcorner[1],grid[1]+1)) and \ - _np.allclose(coords[2],_np.linspace(mincorner[2],maxcorner[2],grid[2]+1)): + if not (_np.allclose(coords[0],_np.linspace(mincorner[0],maxcorner[0],grid[0]+1)) and \ + _np.allclose(coords[1],_np.linspace(mincorner[1],maxcorner[1],grid[1]+1)) and \ + _np.allclose(coords[2],_np.linspace(mincorner[2],maxcorner[2],grid[2]+1))): raise ValueError('Regular grid spacing violated.') - if ordered and not _np.allclose(coord0.reshape(tuple((grid+1)[::-1])+(3,)),node_coord0(grid,size,origin)): - raise ValueError('I_nput data is not a regular grid.') + if ordered and not _np.allclose(coord0.reshape(tuple(grid+1)+(3,),order='F'),node_coord0(grid,size,origin)): + raise ValueError('Input data is not ordered (x fast, z slow).') return (grid,size,origin) @@ -374,15 +402,15 @@ def regrid(size,F,new_grid): Parameters ---------- - size : numpy.ndarray + size : numpy.ndarray of shape (3) physical size - F : numpy.ndarray + F : numpy.ndarray of shape (:,:,:,3,3) deformation gradient field - new_grid : numpy.ndarray + new_grid : numpy.ndarray of shape (3) new grid for undeformed coordinates """ - c = cell_coord0(F.shape[:3][::-1],size) \ + c = cell_coord0(F.shape[:3],size) \ + cell_displacement_avg(size,F) \ + cell_displacement_fluct(size,F) diff --git a/python/tests/test_Result.py b/python/tests/test_Result.py index a90430096..c117f33f7 100644 --- a/python/tests/test_Result.py +++ b/python/tests/test_Result.py @@ -24,6 +24,10 @@ def reference_dir(reference_dir_base): class TestResult: + def test_self_report(self,default): + print(default) + + def test_time_increments(self,default): shape = default.read_dataset(default.get_dataset_location('F'),0).shape default.set_by_time(0.0,20.0) diff --git a/python/tests/test_grid_filters.py b/python/tests/test_grid_filters.py index acbdbf688..eb359006a 100644 --- a/python/tests/test_grid_filters.py +++ b/python/tests/test_grid_filters.py @@ -4,18 +4,18 @@ import numpy as np from damask import grid_filters class TestGridFilters: - + def test_cell_coord0(self): size = np.random.random(3) grid = np.random.randint(8,32,(3)) coord = grid_filters.cell_coord0(grid,size) - assert np.allclose(coord[0,0,0],size/grid*.5) and coord.shape == tuple(grid[::-1]) + (3,) + assert np.allclose(coord[0,0,0],size/grid*.5) and coord.shape == tuple(grid) + (3,) def test_node_coord0(self): size = np.random.random(3) grid = np.random.randint(8,32,(3)) coord = grid_filters.node_coord0(grid,size) - assert np.allclose(coord[-1,-1,-1],size) and coord.shape == tuple(grid[::-1]+1) + (3,) + assert np.allclose(coord[-1,-1,-1],size) and coord.shape == tuple(grid+1) + (3,) def test_coord0(self): size = np.random.random(3) @@ -31,7 +31,7 @@ class TestGridFilters: size = np.random.random(3) origin = np.random.random(3) coord0 = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode)) # noqa - _grid,_size,_origin = eval('grid_filters.{}_coord0_gridSizeOrigin(coord0.reshape(-1,3))'.format(mode)) + _grid,_size,_origin = eval('grid_filters.{}_coord0_gridSizeOrigin(coord0.reshape(-1,3,order="F"))'.format(mode)) assert np.allclose(grid,_grid) and np.allclose(size,_size) and np.allclose(origin,_origin) def test_displacement_fluct_equivalence(self): @@ -57,9 +57,9 @@ class TestGridFilters: shifted = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode)) unshifted = eval('grid_filters.{}_coord0(grid,size)'.format(mode)) if mode == 'cell': - assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid[::-1]) +(3,))) + assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid) +(3,))) elif mode == 'node': - assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid[::-1]+1)+(3,))) + assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid+1)+(3,))) @pytest.mark.parametrize('function',[grid_filters.cell_displacement_avg, grid_filters.node_displacement_avg]) @@ -80,8 +80,43 @@ class TestGridFilters: F = np.broadcast_to(np.random.random((3,3)), tuple(grid)+(3,3)) assert np.allclose(function(size,F),0.0) + @pytest.mark.parametrize('function',[grid_filters.coord0_check, + grid_filters.node_coord0_gridSizeOrigin, + grid_filters.cell_coord0_gridSizeOrigin]) + def test_invalid_coordinates(self,function): + invalid_coordinates = np.random.random((np.random.randint(12,52),3)) + with pytest.raises(ValueError): + function(invalid_coordinates) + + @pytest.mark.parametrize('function',[grid_filters.node_coord0_gridSizeOrigin, + grid_filters.cell_coord0_gridSizeOrigin]) + def test_uneven_spaced_coordinates(self,function): + start = np.random.random(3) + end = np.random.random(3)*10. + start + grid = np.random.randint(8,32,(3)) + uneven = np.stack(np.meshgrid(np.logspace(start[0],end[0],grid[0]), + np.logspace(start[1],end[1],grid[1]), + np.logspace(start[2],end[2],grid[2]),indexing = 'ij'), + axis = -1).reshape((grid.prod(),3),order='F') + with pytest.raises(ValueError): + function(uneven) + + @pytest.mark.parametrize('mode',[True,False]) + @pytest.mark.parametrize('function',[grid_filters.node_coord0_gridSizeOrigin, + grid_filters.cell_coord0_gridSizeOrigin]) + def test_unordered_coordinates(self,function,mode): + origin = np.random.random(3) + size = np.random.random(3)*10.+origin + grid = np.random.randint(8,32,(3)) + unordered = grid_filters.node_coord0(grid,size,origin).reshape(-1,3) + if mode: + with pytest.raises(ValueError): + function(unordered,mode) + else: + function(unordered,mode) + def test_regrid(self): size = np.random.random(3) grid = np.random.randint(8,32,(3)) - F = np.broadcast_to(np.eye(3), tuple(grid[::-1])+(3,3)) + F = np.broadcast_to(np.eye(3), tuple(grid)+(3,3)) assert all(grid_filters.regrid(size,F,grid) == np.arange(grid.prod())) diff --git a/src/homogenization.f90 b/src/homogenization.f90 index 8b6d80089..62150899e 100644 --- a/src/homogenization.f90 +++ b/src/homogenization.f90 @@ -184,8 +184,6 @@ subroutine materialpoint_stressAndItsTangent(updateJaco,dt) e, & !< element number mySource, & myNgrains - real(pReal), dimension(3,3) :: & - subF real(pReal), dimension(discretization_nIP,discretization_nElem) :: & subFrac, & subStep @@ -376,16 +374,15 @@ subroutine materialpoint_stressAndItsTangent(updateJaco,dt) !-------------------------------------------------------------------------------------------------- ! deformation partitioning -! based on materialpoint_subF0,.._subF,crystallite_partionedF0, and homogenization_state, -! results in crystallite_partionedF - !$OMP PARALLEL DO PRIVATE(myNgrains,subF) + !$OMP PARALLEL DO PRIVATE(myNgrains) elementLooping2: do e = FEsolving_execElem(1),FEsolving_execElem(2) myNgrains = homogenization_Ngrains(material_homogenizationAt(e)) IpLooping2: do i = FEsolving_execIP(1),FEsolving_execIP(2) if(requested(i,e) .and. .not. doneAndHappy(1,i,e)) then ! requested but not yet done - subF = materialpoint_F0(1:3,1:3,i,e) & - + (materialpoint_F(1:3,1:3,i,e)-materialpoint_F0(1:3,1:3,i,e))*(subStep(i,e)+subFrac(i,e)) - call partitionDeformation(subF,i,e) ! partition deformation onto constituents + call partitionDeformation(materialpoint_F0(1:3,1:3,i,e) & + + (materialpoint_F(1:3,1:3,i,e)-materialpoint_F0(1:3,1:3,i,e))& + *(subStep(i,e)+subFrac(i,e)), & + i,e) crystallite_dt(1:myNgrains,i,e) = dt*subStep(i,e) ! propagate materialpoint dt to grains crystallite_requested(1:myNgrains,i,e) = .true. ! request calculation for constituents else @@ -397,23 +394,22 @@ subroutine materialpoint_stressAndItsTangent(updateJaco,dt) !-------------------------------------------------------------------------------------------------- ! crystallite integration -! based on crystallite_partionedF0,.._partionedF -! incrementing by crystallite_dt - converged = crystallite_stress() !ToDo: MD not sure if that is the best logic !-------------------------------------------------------------------------------------------------- ! state update - !$OMP PARALLEL DO PRIVATE(subF) + !$OMP PARALLEL DO elementLooping3: do e = FEsolving_execElem(1),FEsolving_execElem(2) IpLooping3: do i = FEsolving_execIP(1),FEsolving_execIP(2) if (requested(i,e) .and. .not. doneAndHappy(1,i,e)) then if (.not. converged(i,e)) then doneAndHappy(1:2,i,e) = [.true.,.false.] else - subF = materialpoint_F0(1:3,1:3,i,e) & - + (materialpoint_F(1:3,1:3,i,e)-materialpoint_F0(1:3,1:3,i,e))*(subStep(i,e)+subFrac(i,e)) - doneAndHappy(1:2,i,e) = updateState(dt*subStep(i,e),subF,i,e) + doneAndHappy(1:2,i,e) = updateState(dt*subStep(i,e), & + materialpoint_F0(1:3,1:3,i,e) & + + (materialpoint_F(1:3,1:3,i,e)-materialpoint_F0(1:3,1:3,i,e)) & + *(subStep(i,e)+subFrac(i,e)), & + i,e) converged(i,e) = all(doneAndHappy(1:2,i,e)) ! converged if done and happy endif endif diff --git a/src/quaternions.f90 b/src/quaternions.f90 index 8d62fe6aa..991f970ab 100644 --- a/src/quaternions.f90 +++ b/src/quaternions.f90 @@ -63,27 +63,27 @@ module quaternions module procedure assign_quat__ module procedure assign_vec__ end interface assignment (=) - + interface quaternion module procedure init__ end interface quaternion - + interface abs procedure abs__ end interface abs - + interface dot_product procedure dot_product__ end interface dot_product - + interface conjg module procedure conjg__ end interface conjg - + interface exp module procedure exp__ end interface exp - + interface log module procedure log__ end interface log @@ -95,7 +95,7 @@ module quaternions interface aimag module procedure aimag__ end interface aimag - + public :: & quaternions_init, & assignment(=), & @@ -118,7 +118,7 @@ end subroutine quaternions_init !--------------------------------------------------------------------------------------------------- -!> construct a quaternion from a 4-vector +!> @brief construct a quaternion from a 4-vector !--------------------------------------------------------------------------------------------------- type(quaternion) pure function init__(array) @@ -133,7 +133,7 @@ end function init__ !--------------------------------------------------------------------------------------------------- -!> assign a quaternion +!> @brief assign a quaternion !--------------------------------------------------------------------------------------------------- elemental pure subroutine assign_quat__(self,other) @@ -141,12 +141,12 @@ elemental pure subroutine assign_quat__(self,other) type(quaternion), intent(in) :: other self = [other%w,other%x,other%y,other%z] - + end subroutine assign_quat__ !--------------------------------------------------------------------------------------------------- -!> assign a 4-vector +!> @brief assign a 4-vector !--------------------------------------------------------------------------------------------------- pure subroutine assign_vec__(self,other) @@ -162,7 +162,7 @@ end subroutine assign_vec__ !--------------------------------------------------------------------------------------------------- -!> add a quaternion +!> @brief add a quaternion !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function add__(self,other) @@ -170,24 +170,24 @@ type(quaternion) elemental pure function add__(self,other) add__ = [ self%w, self%x, self%y ,self%z] & + [other%w, other%x, other%y,other%z] - + end function add__ !--------------------------------------------------------------------------------------------------- -!> return (unary positive operator) +!> @brief return (unary positive operator) !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function pos__(self) class(quaternion), intent(in) :: self pos__ = self * (+1.0_pReal) - + end function pos__ !--------------------------------------------------------------------------------------------------- -!> subtract a quaternion +!> @brief subtract a quaternion !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function sub__(self,other) @@ -195,24 +195,24 @@ type(quaternion) elemental pure function sub__(self,other) sub__ = [ self%w, self%x, self%y ,self%z] & - [other%w, other%x, other%y,other%z] - + end function sub__ !--------------------------------------------------------------------------------------------------- -!> negate (unary negative operator) +!> @brief negate (unary negative operator) !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function neg__(self) class(quaternion), intent(in) :: self neg__ = self * (-1.0_pReal) - + end function neg__ !--------------------------------------------------------------------------------------------------- -!> multiply with a quaternion +!> @brief multiply with a quaternion !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function mul_quat__(self,other) @@ -227,7 +227,7 @@ end function mul_quat__ !--------------------------------------------------------------------------------------------------- -!> multiply with a scalar +!> @brief multiply with a scalar !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function mul_scal__(self,scal) @@ -235,12 +235,12 @@ type(quaternion) elemental pure function mul_scal__(self,scal) real(pReal), intent(in) :: scal mul_scal__ = [self%w,self%x,self%y,self%z]*scal - + end function mul_scal__ !--------------------------------------------------------------------------------------------------- -!> divide by a quaternion +!> @brief divide by a quaternion !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function div_quat__(self,other) @@ -252,7 +252,7 @@ end function div_quat__ !--------------------------------------------------------------------------------------------------- -!> divide by a scalar +!> @brief divide by a scalar !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function div_scal__(self,scal) @@ -265,7 +265,7 @@ end function div_scal__ !--------------------------------------------------------------------------------------------------- -!> test equality +!> @brief test equality !--------------------------------------------------------------------------------------------------- logical elemental pure function eq__(self,other) @@ -278,7 +278,7 @@ end function eq__ !--------------------------------------------------------------------------------------------------- -!> test inequality +!> @brief test inequality !--------------------------------------------------------------------------------------------------- logical elemental pure function neq__(self,other) @@ -290,7 +290,7 @@ end function neq__ !--------------------------------------------------------------------------------------------------- -!> raise to the power of a quaternion +!> @brief raise to the power of a quaternion !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function pow_quat__(self,expon) @@ -303,7 +303,7 @@ end function pow_quat__ !--------------------------------------------------------------------------------------------------- -!> raise to the power of a scalar +!> @brief raise to the power of a scalar !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function pow_scal__(self,expon) @@ -316,7 +316,7 @@ end function pow_scal__ !--------------------------------------------------------------------------------------------------- -!> take exponential +!> @brief take exponential !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function exp__(a) @@ -336,7 +336,7 @@ end function exp__ !--------------------------------------------------------------------------------------------------- -!> take logarithm +!> @brief take logarithm !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function log__(a) @@ -356,7 +356,7 @@ end function log__ !--------------------------------------------------------------------------------------------------- -!> return norm +!> @brief return norm !--------------------------------------------------------------------------------------------------- real(pReal) elemental pure function abs__(self) @@ -368,7 +368,7 @@ end function abs__ !--------------------------------------------------------------------------------------------------- -!> calculate dot product +!> @brief calculate dot product !--------------------------------------------------------------------------------------------------- real(pReal) elemental pure function dot_product__(a,b) @@ -380,7 +380,7 @@ end function dot_product__ !--------------------------------------------------------------------------------------------------- -!> take conjugate complex +!> @brief take conjugate complex !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function conjg__(self) @@ -392,7 +392,7 @@ end function conjg__ !--------------------------------------------------------------------------------------------------- -!> homomorph +!> @brief homomorph !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function homomorphed(self) @@ -404,7 +404,7 @@ end function homomorphed !--------------------------------------------------------------------------------------------------- -!> return as plain array +!> @brief return as plain array !--------------------------------------------------------------------------------------------------- pure function asArray(self) @@ -417,7 +417,7 @@ end function asArray !--------------------------------------------------------------------------------------------------- -!> real part (scalar) +!> @brief real part (scalar) !--------------------------------------------------------------------------------------------------- pure function real__(self) @@ -430,7 +430,7 @@ end function real__ !--------------------------------------------------------------------------------------------------- -!> imaginary part (3-vector) +!> @brief imaginary part (3-vector) !--------------------------------------------------------------------------------------------------- pure function aimag__(self) @@ -443,7 +443,7 @@ end function aimag__ !--------------------------------------------------------------------------------------------------- -!> inverse +!> @brief inverse !--------------------------------------------------------------------------------------------------- type(quaternion) elemental pure function inverse(self)