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DAMASK_EICMD
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Merge branch 'misc-improvements' into 'development' 

Misc improvements

See merge request damask/DAMASK!300
This commit is contained in:
Sharan Roongta 2020-12-11 18:13:46 +01:00
parent f5f2cdba7b 8c8dd9ba0a
commit ca71b73799
9 changed files with 57 additions and 205 deletions
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23
Makefile
View File

@ -2,27 +2,20 @@ SHELL = /bin/sh
########################################################################################
# Makefile for the installation of DAMASK
########################################################################################
DAMASK_ROOT = $(shell python3 -c "import os,sys; print(os.path.normpath(os.path.realpath(os.path.expanduser('$(pwd)'))))")
.PHONY: all
all: grid mesh processing
.PHONY: grid
grid: build/grid
@(cd build/grid;make -j${DAMASK_NUM_THREADS} all install;)
grid:
@cmake -B build/grid -DDAMASK_SOLVER=GRID -DCMAKE_INSTALL_PREFIX=${PWD} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP}
@cmake --build build/grid --parallel ${DAMASK_NUM_THRADS}
@cmake --install build/grid
.PHONY: mesh
mesh: build/mesh
@(cd build/mesh; make -j${DAMASK_NUM_THREADS} all install;)
.PHONY: build/grid
build/grid:
@mkdir -p build/grid
@(cd build/grid; cmake -Wno-dev -DDAMASK_SOLVER=GRID -DCMAKE_INSTALL_PREFIX=${DAMASK_ROOT} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP} ../../;)
.PHONY: build/mesh
build/mesh:
@mkdir -p build/mesh
@(cd build/mesh; cmake -Wno-dev -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${DAMASK_ROOT} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP} ../../;)
mesh:
@cmake -B build/mesh -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${PWD} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP}
@cmake --build build/mesh --parallel ${DAMASK_NUM_THRADS}
@cmake --install build/mesh
.PHONY: clean
clean:

2
PRIVATE

@ -1 +1 @@
Subproject commit fd99d76d1eaa42fd36971ff2f79a59d98534fc27
Subproject commit 08f8aea465a1b5e476b584bcae7927d113919b1d

2
python/damask/_colormap.py
View File

@ -57,7 +57,7 @@ class Colormap(mpl.colors.ListedColormap):
ax1.imshow(np.linspace(0,1,self.N).reshape(1,-1),
aspect='auto', cmap=self, interpolation='nearest')
plt.show(block = False)
return self.name
return 'Colormap: '+self.name
@staticmethod

38
python/damask/_grid.py
View File

@ -7,7 +7,8 @@ import warnings
import numpy as np
import pandas as pd
import h5py
from scipy import ndimage,spatial
from scipy import ndimage, spatial
from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
from . import environment
from . import VTK
@ -43,12 +44,15 @@ class Grid:
def __repr__(self):
"""Basic information on grid definition."""
mat_min = np.nanmin(self.material)
mat_max = np.nanmax(self.material)
mat_N = self.N_materials
return util.srepr([
f'cells a b c: {util.srepr(self.cells, " x ")}',
f'size x y z: {util.srepr(self.size, " x ")}',
f'origin x y z: {util.srepr(self.origin," ")}',
f'# materials: {self.N_materials}',
f'max material: {np.nanmax(self.material)}',
f'cells a b c: {util.srepr(self.cells, " x ")}',
f'size x y z: {util.srepr(self.size, " x ")}',
f'origin x y z: {util.srepr(self.origin," ")}',
f'# materials: {mat_N}' + ('' if mat_min == 0 and mat_max+1 == mat_N else
f' (min: {mat_min}, max: {mat_max})')
])
@ -104,9 +108,9 @@ class Grid:
@material.setter
def material(self,material):
if len(material.shape) != 3:
raise ValueError(f'Invalid material shape {material.shape}.')
raise ValueError(f'invalid material shape {material.shape}')
elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
raise TypeError(f'Invalid material data type {material.dtype}.')
raise TypeError(f'invalid material data type {material.dtype}')
else:
self._material = np.copy(material)
@ -123,7 +127,7 @@ class Grid:
@size.setter
def size(self,size):
if len(size) != 3 or any(np.array(size) <= 0):
raise ValueError(f'Invalid size {size}.')
raise ValueError(f'invalid size {size}')
else:
self._size = np.array(size)
@ -135,7 +139,7 @@ class Grid:
@origin.setter
def origin(self,origin):
if len(origin) != 3:
raise ValueError(f'Invalid origin {origin}.')
raise ValueError(f'invalid origin {origin}')
else:
self._origin = np.array(origin)
@ -178,6 +182,10 @@ class Grid:
cells = np.array(v.vtk_data.GetDimensions())-1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
for i,c in enumerate([v.vtk_data.GetXCoordinates(),v.vtk_data.GetYCoordinates(),v.vtk_data.GetZCoordinates()]):
if not np.allclose(vtk_to_np(c),np.linspace(bbox[0][i],bbox[1][i],cells[i]+1)):
raise ValueError('regular grid spacing violated')
return Grid(material = v.get('material').reshape(cells,order='F'),
size = bbox[1] - bbox[0],
origin = bbox[0],
@ -211,7 +219,7 @@ class Grid:
except ValueError:
header_length,keyword = (-1, 'invalid')
if not keyword.startswith('head') or header_length < 3:
raise TypeError('Header length information missing or invalid')
raise TypeError('header length information missing or invalid')
comments = []
content = f.readlines()
@ -243,7 +251,7 @@ class Grid:
i += len(items)
if i != cells.prod():
raise TypeError(f'Invalid file: expected {cells.prod()} entries, found {i}')
raise TypeError(f'invalid file: expected {cells.prod()} entries, found {i}')
if not np.any(np.mod(material,1) != 0.0): # no float present
material = material.astype('int') - (1 if material.min() > 0 else 0)
@ -628,7 +636,7 @@ class Grid:
"""
valid = ['x','y','z']
if not set(directions).issubset(valid):
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
limits = [None,None] if reflect else [-2,0]
mat = self.material.copy()
@ -660,7 +668,7 @@ class Grid:
"""
valid = ['x','y','z']
if not set(directions).issubset(valid):
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
mat = np.flip(self.material, (valid.index(d) for d in directions if d in valid))
@ -913,7 +921,7 @@ class Grid:
"""
valid = ['x','y','z']
if not set(directions).issubset(valid):
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
o = [[0, self.cells[0]+1, np.prod(self.cells[:2]+1)+self.cells[0]+1, np.prod(self.cells[:2]+1)],
[0, np.prod(self.cells[:2]+1), np.prod(self.cells[:2]+1)+1, 1],

9
python/damask/_result.py
View File

@ -784,7 +784,7 @@ class Result:
@staticmethod
def _add_IPF_color(q,l):
def _add_IPF_color(l,q):
m = util.scale_to_coprime(np.array(l))
try:
lattice = {'fcc':'cF','bcc':'cI','hex':'hP'}[q['meta']['Lattice']]
@ -805,16 +805,17 @@ class Result:
'Creator': 'add_IPF_color'
}
}
def add_IPF_color(self,q,l):
def add_IPF_color(self,l,q='O'):
"""
Add RGB color tuple of inverse pole figure (IPF) color.
Parameters
----------
q : str
Label of the dataset containing the crystallographic orientation as quaternions.
l : numpy.array of shape (3)
Lab frame direction for inverse pole figure.
q : str
Label of the dataset containing the crystallographic orientation as quaternions.
Defaults to 'O'.
"""
self._add_generic_pointwise(self._add_IPF_color,{'q':q},{'l':l})

7
python/damask/_vtk.py
View File

@ -76,7 +76,8 @@ class VTK:
nodes : numpy.ndarray of shape (:,3)
Spatial position of the nodes.
connectivity : numpy.ndarray of np.dtype = int
Cell connectivity (0-based), first dimension determines #Cells, second dimension determines #Nodes/Cell.
Cell connectivity (0-based), first dimension determines #Cells,
second dimension determines #Nodes/Cell.
cell_type : str
Name of the vtk.vtkCell subclass. Tested for TRIANGLE, QUAD, TETRA, and HEXAHEDRON.
@ -91,7 +92,9 @@ class VTK:
vtk_data = vtk.vtkUnstructuredGrid()
vtk_data.SetPoints(vtk_nodes)
vtk_data.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
cell_types = {'TRIANGLE':vtk.VTK_TRIANGLE, 'QUAD':vtk.VTK_QUAD,
'TETRA' :vtk.VTK_TETRA, 'HEXAHEDRON':vtk.VTK_HEXAHEDRON}
vtk_data.SetCells(cell_types[cell_type.split("_",1)[-1].upper()],cells)
return VTK(vtk_data)

13
python/tests/test_Grid.py
View File

@ -1,5 +1,6 @@
import pytest
import numpy as np
from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk
from damask import VTK
from damask import Grid
@ -57,13 +58,21 @@ class TestGrid:
new = Grid.load(tmp_path/'default.vtr')
assert grid_equal(new,default)
def test_invalid_vtr(self,tmp_path):
def test_invalid_no_material(self,tmp_path):
v = VTK.from_rectilinear_grid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
v.save(tmp_path/'no_materialpoint.vtr',parallel=False)
with pytest.raises(ValueError):
Grid.load(tmp_path/'no_materialpoint.vtr')
def test_invalid_material(self):
def test_invalid_spacing(self,tmp_path,default):
default.save(tmp_path/'spacing_ok.vtr')
vtk = VTK.load(tmp_path/'spacing_ok.vtr')
vtk.vtk_data.SetXCoordinates(np_to_vtk(np.sort(np.random.random(default.cells[0]))))
vtk.save(tmp_path/'invalid_spacing.vtr',parallel=False)
with pytest.raises(ValueError):
Grid.load(tmp_path/'invalid_spacing.vtr')
def test_invalid_material_type(self):
with pytest.raises(TypeError):
Grid(np.zeros((3,3,3),dtype='complex'),np.ones(3))

2
python/tests/test_Result.py
View File

@ -169,7 +169,7 @@ class TestResult:
@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('O',np.array(d))
default.add_IPF_color(d,'O')
loc = {'O': default.get_dataset_location('O'),
'color': default.get_dataset_location('IPFcolor_[{} {} {}]'.format(*d))}
qu = default.read_dataset(loc['O']).view(np.double).squeeze()

166
src/grid/discretization_grid.f90
View File

@ -149,168 +149,6 @@ subroutine discretization_grid_init(restart)
end subroutine discretization_grid_init
!--------------------------------------------------------------------------------------------------
!> @brief Parses geometry file
!> @details important variables have an implicit "save" attribute. Therefore, this function is
! supposed to be called only once!
!--------------------------------------------------------------------------------------------------
subroutine readGeom(grid,geomSize,origin,material)
integer, dimension(3), intent(out) :: &
grid ! grid (across all processes!)
real(pReal), dimension(3), intent(out) :: &
geomSize, & ! size (across all processes!)
origin ! origin (across all processes!)
integer, dimension(:), intent(out), allocatable :: &
material
character(len=:), allocatable :: rawData
character(len=65536) :: line
integer, allocatable, dimension(:) :: chunkPos
integer :: &
headerLength = -1, & !< length of header (in lines)
fileLength, & !< length of the geom file (in characters)
fileUnit, &
startPos, endPos, &
myStat, &
l, & !< line counter
c, & !< counter for # materials in line
o, & !< order of "to" packing
e, & !< "element", i.e. spectral collocation point
i, j
grid = -1
geomSize = -1.0_pReal
!--------------------------------------------------------------------------------------------------
! read raw data as stream
inquire(file = trim(interface_geomFile), size=fileLength)
open(newunit=fileUnit, file=trim(interface_geomFile), access='stream',&
status='old', position='rewind', action='read',iostat=myStat)
if(myStat /= 0) call IO_error(100,ext_msg=trim(interface_geomFile))
allocate(character(len=fileLength)::rawData)
read(fileUnit) rawData
close(fileUnit)
!--------------------------------------------------------------------------------------------------
! get header length
endPos = index(rawData,IO_EOL)
if(endPos <= index(rawData,'head')) then ! ToDo: Should be 'header'
startPos = len(rawData)
call IO_error(error_ID=841, ext_msg='readGeom')
else
chunkPos = IO_stringPos(rawData(1:endPos))
if (chunkPos(1) < 2) call IO_error(error_ID=841, ext_msg='readGeom')
headerLength = IO_intValue(rawData(1:endPos),chunkPos,1)
startPos = endPos + 1
endif
!--------------------------------------------------------------------------------------------------
! read and interpret header
origin = 0.0_pReal
l = 0
do while (l < headerLength .and. startPos < len(rawData))
endPos = startPos + index(rawData(startPos:),IO_EOL) - 1
if (endPos < startPos) endPos = len(rawData) ! end of file without new line
line = rawData(startPos:endPos)
startPos = endPos + 1
l = l + 1
chunkPos = IO_stringPos(trim(line))
if (chunkPos(1) < 2) cycle ! need at least one keyword value pair
select case (IO_lc(IO_StringValue(trim(line),chunkPos,1)) )
case ('grid')
if (chunkPos(1) > 6) then
do j = 2,6,2
select case (IO_lc(IO_stringValue(line,chunkPos,j)))
case('a')
grid(1) = IO_intValue(line,chunkPos,j+1)
case('b')
grid(2) = IO_intValue(line,chunkPos,j+1)
case('c')
grid(3) = IO_intValue(line,chunkPos,j+1)
end select
enddo
endif
case ('size')
if (chunkPos(1) > 6) then
do j = 2,6,2
select case (IO_lc(IO_stringValue(line,chunkPos,j)))
case('x')
geomSize(1) = IO_floatValue(line,chunkPos,j+1)
case('y')
geomSize(2) = IO_floatValue(line,chunkPos,j+1)
case('z')
geomSize(3) = IO_floatValue(line,chunkPos,j+1)
end select
enddo
endif
case ('origin')
if (chunkPos(1) > 6) then
do j = 2,6,2
select case (IO_lc(IO_stringValue(line,chunkPos,j)))
case('x')
origin(1) = IO_floatValue(line,chunkPos,j+1)
case('y')
origin(2) = IO_floatValue(line,chunkPos,j+1)
case('z')
origin(3) = IO_floatValue(line,chunkPos,j+1)
end select
enddo
endif
end select
enddo
!--------------------------------------------------------------------------------------------------
! sanity checks
if(any(grid < 1)) &
call IO_error(error_ID = 842, ext_msg='grid (readGeom)')
if(any(geomSize < 0.0_pReal)) &
call IO_error(error_ID = 842, ext_msg='size (readGeom)')
allocate(material(product(grid)), source = -1) ! too large in case of MPI (shrink later, not very elegant)
!--------------------------------------------------------------------------------------------------
! read and interpret content
e = 1
do while (startPos < len(rawData))
endPos = startPos + index(rawData(startPos:),IO_EOL) - 1
if (endPos < startPos) endPos = len(rawData) ! end of file without new line
line = rawData(startPos:endPos)
startPos = endPos + 1
l = l + 1
chunkPos = IO_stringPos(trim(line))
noCompression: if (chunkPos(1) /= 3) then
c = chunkPos(1)
material(e:e+c-1) = [(IO_intValue(line,chunkPos,i+1), i=0, c-1)]
else noCompression
compression: if (IO_lc(IO_stringValue(line,chunkPos,2)) == 'of') then
c = IO_intValue(line,chunkPos,1)
material(e:e+c-1) = [(IO_intValue(line,chunkPos,3),i = 1,IO_intValue(line,chunkPos,1))]
else if (IO_lc(IO_stringValue(line,chunkPos,2)) == 'to') then compression
c = abs(IO_intValue(line,chunkPos,3) - IO_intValue(line,chunkPos,1)) + 1
o = merge(+1, -1, IO_intValue(line,chunkPos,3) > IO_intValue(line,chunkPos,1))
material(e:e+c-1) = [(i, i = IO_intValue(line,chunkPos,1),IO_intValue(line,chunkPos,3),o)]
else compression
c = chunkPos(1)
material(e:e+c-1) = [(IO_intValue(line,chunkPos,i+1), i=0, c-1)]
endif compression
endif noCompression
e = e+c
end do
if (e-1 /= product(grid)) call IO_error(error_ID = 843, el=e)
end subroutine readGeom
!--------------------------------------------------------------------------------------------------
!> @brief Parse vtk rectilinear grid (.vtr)
!> @details https://vtk.org/Wiki/VTK_XML_Formats
@ -566,12 +404,12 @@ subroutine readVTR(grid,geomSize,origin,material)
size_deflated = temp(4:)
bytes_inflated = base64_to_bytes(base64_str(base64_nChar(headerLen)+1_pI64:))
allocate(bytes(0))
allocate(bytes(sum(size_inflated)))
e = 0_pI64
do b = 1, nBlock
s = e + 1_pI64
e = s + size_deflated(b) - 1_pI64
bytes = [bytes,zlib_inflate(bytes_inflated(s:e),size_inflated(b))]
bytes(sum(size_inflated(:b-1))+1_pI64:sum(size_inflated(:b))) = zlib_inflate(bytes_inflated(s:e),size_inflated(b))
enddo
end function asBytes_compressed