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Merge branch 'development' into YAML-compatible-numerics

This commit is contained in:
Sharan Roongta 2020-06-25 11:02:13 +02:00
parent e155bef9a5 ff858fd4c8
commit 78b6b3ecdb
23 changed files with 450 additions and 301 deletions
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2
VERSION
View File

@ -1 +1 @@
v2.0.3-2650-g512e54a7
v2.0.3-2692-g3d93a5ff

2
examples/ConfigFiles/Phase_DisloUCLA_Tungsten.config
View File

@ -27,7 +27,7 @@ SolidSolutionStrength 0.0 # Strength due to elements in solid solution
### Dislocation glide parameters ###
#per family
Nslip 12 0
Nslip 12
slipburgers 2.72e-10 # Burgers vector of slip system [m]
rhoedge0 1.0e12 # Initial edge dislocation density [m/m**3]
rhoedgedip0 1.0 # Initial edged dipole dislocation density [m/m**3]

56
installation/symlink_Processing.py
View File

@ -1,56 +1,30 @@
#!/usr/bin/env python3
# Makes postprocessing routines accessible from everywhere.
import os
import sys
from pathlib import Path
import damask
damaskEnv = damask.Environment()
baseDir = damaskEnv.relPath('processing/')
binDir = damaskEnv.relPath('bin/')
env = damask.Environment()
bin_dir = env.root_dir/Path('bin')
if not os.path.isdir(binDir):
os.mkdir(binDir)
if not bin_dir.exists():
bin_dir.mkdir()
#define ToDo list
processing_subDirs = ['pre',
'post',
]
sys.stdout.write('\nsymbolic linking...\n')
for sub_dir in ['pre','post']:
the_dir = env.root_dir/Path('processing')/Path(sub_dir)
for subDir in processing_subDirs:
theDir = os.path.abspath(os.path.join(baseDir,subDir))
sys.stdout.write('\n'+binDir+' ->\n'+theDir+damask.util.deemph(' ...')+'\n')
for theFile in os.listdir(theDir):
theName,theExt = os.path.splitext(theFile)
if theExt in ['.py']:
src = os.path.abspath(os.path.join(theDir,theFile))
sym_link = os.path.abspath(os.path.join(binDir,theName))
if os.path.lexists(sym_link):
os.remove(sym_link)
output = theName+damask.util.deemph(theExt)
else:
output = damask.util.emph(theName)+damask.util.deemph(theExt)
sys.stdout.write(damask.util.deemph('... ')+output+'\n')
os.symlink(src,sym_link)
for the_file in the_dir.glob('*.py'):
src = the_dir/the_file
dst = bin_dir/Path(the_file.with_suffix('').name)
if dst.is_file(): dst.unlink() # dst.unlink(True) for Python >3.8
dst.symlink_to(src)
sys.stdout.write('\npruning broken links...\n')
brokenLinks = 0
for filename in os.listdir(binDir):
path = os.path.join(binDir,filename)
if os.path.islink(path) and not os.path.exists(path):
sys.stdout.write(' '+damask.util.delete(path)+'\n')
os.remove(path)
brokenLinks += 1
sys.stdout.write(('none.' if brokenLinks == 0 else '')+'\n')
for filename in bin_dir.glob('*'):
if not filename.is_file():
filename.unlink

25
processing/pre/mentat_pbcOnBoxMesh.py
View File

@ -6,7 +6,7 @@ import numpy as np
from optparse import OptionParser
import damask
sys.path.append(damask.solver.Marc().libraryPath())
sys.path.append(str(damask.solver.Marc().library_path))
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -197,14 +197,15 @@ def add_servoLinks(mfd_data,active=[True,True,True]): # directions on which to
if mfd_data[i]['uid'] == 1705: del mfd_data[i]
mfd_data.insert(i, links)
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Set up servo linking to achieve periodic boundary conditions for a regular hexahedral mesh.
Use *py_connection to operate on model presently opened in MSC.Mentat.
""", version = scriptID)
parser.add_option('-p', '--port',
@ -229,10 +230,7 @@ if remote and filenames != []:
if filenames == []: filenames = [None]
if remote:
try: import py_mentat
except:
damask.util.croak('no valid Mentat release found.')
sys.exit(-1)
import py_mentat
damask.util.report(scriptName, 'waiting to connect...')
filenames = [os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()) + '.mfd')]
@ -240,14 +238,14 @@ if remote:
py_mentat.py_connect('',options.port)
py_mentat.py_send('*set_save_formatted on')
py_mentat.py_send('*save_as_model "{}" yes'.format(filenames[0]))
py_mentat.py_get_int("nnodes()") # hopefully blocks until file is written
except:
damask.util.croak('failed. try setting Tools/Python/"Run as Separate Process" & "Initiate".')
sys.exit()
py_mentat.py_get_int("nnodes()")
except py_mentat.InputError as err:
damask.util.croak('{}. Try Tools/Python/"Run as Separate Process" & "Initiate".'.format(err))
sys.exit(-1)
damask.util.croak( 'connected...')
for name in filenames:
while remote and not os.path.exists(name): time.sleep(0.5) # wait for Mentat to write MFD file
while remote and not os.path.exists(name): time.sleep(0.5)
with open( name,'r') if name is not None else sys.stdin as fileIn:
damask.util.report(scriptName, name)
mfd = parseMFD(fileIn)
@ -257,5 +255,4 @@ for name in filenames:
fileOut.write(asMFD(mfd))
if remote:
try: py_mentat.py_send('*open_model "{}"'.format(filenames[0]))
except: damask.util.croak('lost connection on sending open command for "{}".'.format(filenames[0]))
py_mentat.py_send('*open_model "{}"'.format(filenames[0]))

2
processing/pre/mentat_spectralBox.py
View File

@ -9,7 +9,7 @@ import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
sys.path.append(damask.solver.Marc().libraryPath())
sys.path.append(str(damask.solver.Marc().library_path))
#-------------------------------------------------------------------------------------------------
def outMentat(cmd,locals):

4
python/damask/__init__.py
View File

@ -1,9 +1,9 @@
"""Tools for pre and post processing of DAMASK simulations."""
import os as _os
from pathlib import Path as _Path
import re as _re
name = 'damask'
with open(_os.path.join(_os.path.dirname(__file__),'VERSION')) as _f:
with open(_Path(__file__).parent/_Path('VERSION')) as _f:
version = _re.sub(r'^v','',_f.readline().strip())
# make classes directly accessible as damask.Class

25
python/damask/_environment.py
View File

@ -1,11 +1,11 @@
import os
from pathlib import Path
import tkinter
class Environment:
def __init__(self):
"""Read and provide values of DAMASK configuration."""
self.options = self._get_options()
try:
tk = tkinter.Tk()
self.screen_width = tk.winfo_screenwidth()
@ -15,17 +15,8 @@ class Environment:
self.screen_width = 1024
self.screen_height = 768
def relPath(self,relative = '.'):
"""Return absolute path from path relative to DAMASK root."""
return os.path.join(self.rootDir(),relative)
def rootDir(self):
"""Return DAMASK root path."""
return os.path.normpath(os.path.join(os.path.realpath(__file__),'../../../'))
def _get_options(self):
@property
def options(self):
options = {}
for item in ['DAMASK_NUM_THREADS',
'MSC_ROOT',
@ -34,3 +25,13 @@ class Environment:
options[item] = os.environ[item] if item in os.environ else None
return options
@property
def root_dir(self):
"""Return DAMASK root path."""
return Path(__file__).parents[2]
# for compatibility
def rootDir(self):
return str(self.root_dir)

19
python/damask/_result.py
View File

@ -6,6 +6,7 @@ import os
import datetime
import xml.etree.ElementTree as ET
import xml.dom.minidom
from pathlib import Path
from functools import partial
import h5py
@ -88,7 +89,7 @@ class Result:
'con_physics': self.con_physics, 'mat_physics': self.mat_physics
}
self.fname = os.path.abspath(fname)
self.fname = Path(fname).absolute()
self._allow_modification = False
@ -1056,14 +1057,17 @@ class Result:
Parameters
----------
func : function
Callback function that calculates a new dataset from one or more datasets per HDF5 group.
Callback function that calculates a new dataset from one or
more datasets per HDF5 group.
datasets : dictionary
Details of the datasets to be used: label (in HDF5 file) and arg (argument to which the data is parsed in func).
Details of the datasets to be used: label (in HDF5 file) and
arg (argument to which the data is parsed in func).
args : dictionary, optional
Arguments parsed to func.
"""
pool = multiprocessing.Pool(int(Environment().options['DAMASK_NUM_THREADS']))
num_threads = Environment().options['DAMASK_NUM_THREADS']
pool = multiprocessing.Pool(int(num_threads) if num_threads is not None else None)
lock = multiprocessing.Manager().Lock()
groups = self.groups_with_datasets(datasets.values())
@ -1190,7 +1194,7 @@ class Result:
'Dimensions': '{} {} {} {}'.format(*self.grid,np.prod(shape))}
data_items[-1].text='{}:{}'.format(os.path.split(self.fname)[1],name)
with open(os.path.splitext(self.fname)[0]+'.xdmf','w') as f:
with open(self.fname.with_suffix('.xdmf').name,'w') as f:
f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
@ -1266,7 +1270,4 @@ class Result:
u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
v.add(u,'u')
file_out = '{}_inc{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
inc[3:].zfill(N_digits))
v.write(file_out)
v.write('{}_inc{}'.format(self.fname.stem,inc[3:].zfill(N_digits)))

280
python/damask/_rotation.py
View File

@ -20,8 +20,8 @@ class Rotation:
when viewing from the end point of the rotation axis towards the origin.
- rotations will be interpreted in the passive sense.
- Euler angle triplets are implemented using the Bunge convention,
with the angular ranges as [0, 2π],[0, π],[0, 2π].
- the rotation angle ω is limited to the interval [0, π].
with the angular ranges as [0,2π], [0,π], [0,2π].
- the rotation angle ω is limited to the interval [0,π].
- the real part of a quaternion is positive, Re(q) > 0
- P = -1 (as default).
@ -49,7 +49,8 @@ class Rotation:
Parameters
----------
quaternion : numpy.ndarray, optional
Unit quaternion that follows the conventions. Use .from_quaternion to perform a sanity check.
Unit quaternion in positive real hemisphere.
Use .from_quaternion to perform a sanity check.
"""
self.quaternion = quaternion.copy()
@ -73,7 +74,7 @@ class Rotation:
raise NotImplementedError('Support for multiple rotations missing')
return '\n'.join([
'Quaternion: (real={:.3f}, imag=<{:+.3f}, {:+.3f}, {:+.3f}>)'.format(*(self.quaternion)),
'Matrix:\n{}'.format(self.as_matrix()),
'Matrix:\n{}'.format(np.round(self.as_matrix(),8)),
'Bunge Eulers / deg: ({:3.2f}, {:3.2f}, {:3.2f})'.format(*self.as_Eulers(degrees=True)),
])
@ -87,10 +88,6 @@ class Rotation:
other : numpy.ndarray or Rotation
Vector, second or fourth order tensor, or rotation object that is rotated.
Todo
----
Check rotation of 4th order tensor
"""
if isinstance(other, Rotation):
q_m = self.quaternion[...,0:1]
@ -99,7 +96,7 @@ class Rotation:
p_o = other.quaternion[...,1:]
q = (q_m*q_o - np.einsum('...i,...i',p_m,p_o).reshape(self.shape+(1,)))
p = q_m*p_o + q_o*p_m + _P * np.cross(p_m,p_o)
return self.__class__(np.block([q,p])).standardize()
return self.__class__(np.block([q,p]))._standardize()
elif isinstance(other,np.ndarray):
if self.shape + (3,) == other.shape:
@ -124,24 +121,24 @@ class Rotation:
else:
raise TypeError('Cannot rotate {}'.format(type(other)))
def inverse(self):
"""In-place inverse rotation/backward rotation."""
self.quaternion[...,1:] *= -1
return self
def inversed(self):
"""Inverse rotation/backward rotation."""
return self.copy().inverse()
def standardize(self):
"""In-place quaternion representation with positive real part."""
def _standardize(self):
"""Standardize (ensure positive real hemisphere)."""
self.quaternion[self.quaternion[...,0] < 0.0] *= -1
return self
def standardized(self):
"""Quaternion representation with positive real part."""
return self.copy().standardize()
def inverse(self):
"""In-place inverse rotation (backward rotation)."""
self.quaternion[...,1:] *= -1
return self
def __invert__(self):
"""Inverse rotation (backward rotation)."""
return self.copy().inverse()
def inversed(self):
"""Inverse rotation (backward rotation)."""
return ~ self
def misorientation(self,other):
@ -154,7 +151,7 @@ class Rotation:
Rotation to which the misorientation is computed.
"""
return other*self.inversed()
return other@~self
def broadcast_to(self,shape):
@ -169,7 +166,7 @@ class Rotation:
return self.__class__(q)
def average(self,other):
def average(self,other): #ToDo: discuss calling for vectors
"""
Calculate the average rotation.
@ -189,25 +186,31 @@ class Rotation:
def as_quaternion(self):
"""
Unit quaternion [q, p_1, p_2, p_3].
Represent as unit quaternion.
Parameters
----------
quaternion : bool, optional
return quaternion as DAMASK object.
Returns
-------
q : numpy.ndarray of shape (...,4)
Unit quaternion in positive real hemisphere: (q_0, q_1, q_2, q_3), |q|=1, q_0 ≥ 0.
"""
return self.quaternion
return self.quaternion.copy()
def as_Eulers(self,
degrees = False):
"""
Bunge-Euler angles: (φ_1, ϕ, φ_2).
Represent as Bunge-Euler angles.
Parameters
----------
degrees : bool, optional
return angles in degrees.
Return angles in degrees.
Returns
-------
phi : numpy.ndarray of shape (...,3)
Bunge-Euler angles: (φ_1, ϕ, φ_2), φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]
unless degrees == True: φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360]
"""
eu = Rotation._qu2eu(self.quaternion)
@ -218,14 +221,21 @@ class Rotation:
degrees = False,
pair = False):
"""
Axis angle representation [n_1, n_2, n_3, ω] unless pair == True: ([n_1, n_2, n_3], ω).
Represent as axis angle pair.
Parameters
----------
degrees : bool, optional
return rotation angle in degrees.
Return rotation angle in degrees. Defaults to False.
pair : bool, optional
return tuple of axis and angle.
Return tuple of axis and angle. Defaults to False.
Returns
-------
axis_angle : numpy.ndarray of shape (...,4) unless pair == True:
tuple containing numpy.ndarray of shapes (...,3) and (...)
Axis angle pair: (n_1, n_2, n_3, ω), |n| = 1 and ω ∈ [0,π]
unless degrees = True: ω ∈ [0,180].
"""
ax = Rotation._qu2ax(self.quaternion)
@ -233,29 +243,60 @@ class Rotation:
return (ax[...,:3],ax[...,3]) if pair else ax
def as_matrix(self):
"""Rotation matrix."""
"""
Represent as rotation matrix.
Returns
-------
R : numpy.ndarray of shape (...,3,3)
Rotation matrix R, det(R) = 1, R.T∙R=I.
"""
return Rotation._qu2om(self.quaternion)
def as_Rodrigues(self,
vector = False):
"""
Rodrigues-Frank vector representation [n_1, n_2, n_3, tan(ω/2)] unless vector == True: [n_1, n_2, n_3] * tan(ω/2).
Represent as Rodrigues-Frank vector with separated axis and angle argument.
Parameters
----------
vector : bool, optional
return as actual Rodrigues--Frank vector, i.e. rotation axis scaled by tan(ω/2).
Return as actual Rodrigues-Frank vector, i.e. axis
and angle argument are not separated.
Returns
-------
rho : numpy.ndarray of shape (...,4) unless vector == True:
numpy.ndarray of shape (...,3)
Rodrigues-Frank vector: [n_1, n_2, n_3, tan(ω/2)], |n| = 1 and ω ∈ [0,π].
"""
ro = Rotation._qu2ro(self.quaternion)
return ro[...,:3]*ro[...,3] if vector else ro
def as_homochoric(self):
"""Homochoric vector: (h_1, h_2, h_3)."""
"""
Represent as homochoric vector.
Returns
-------
h : numpy.ndarray of shape (...,3)
Homochoric vector: (h_1, h_2, h_3), |h| < 1/2*π^(2/3).
"""
return Rotation._qu2ho(self.quaternion)
def as_cubochoric(self):
"""Cubochoric vector: (c_1, c_2, c_3)."""
"""
Represent as cubochoric vector.
Returns
-------
c : numpy.ndarray of shape (...,3)
Cubochoric vector: (c_1, c_2, c_3), max(c_i) < 1/2*π^(2/3).
"""
return Rotation._qu2cu(self.quaternion)
def M(self): # ToDo not sure about the name: as_M or M? we do not have a from_M
@ -275,18 +316,34 @@ class Rotation:
# Static constructors. The input data needs to follow the conventions, options allow to
# relax the conventions.
@staticmethod
def from_quaternion(quaternion,
def from_quaternion(q,
accept_homomorph = False,
P = -1,
acceptHomomorph = None):
acceptHomomorph = None): # old name (for compatibility)
"""
Initialize from quaternion.
Parameters
----------
q : numpy.ndarray of shape (...,4)
Unit quaternion in positive real hemisphere: (q_0, q_1, q_2, q_3),
|q|=1, q_0 ≥ 0.
accept_homomorph : boolean, optional
Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
Defaults to False.
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
if acceptHomomorph is not None:
accept_homomorph = acceptHomomorph
qu = np.array(quaternion,dtype=float)
accept_homomorph = acceptHomomorph # for compatibility
qu = np.array(q,dtype=float)
if qu.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if P > 0: qu[...,1:4] *= -1 # convert from P=1 to P=-1
if P == 1: qu[...,1:4] *= -1
if accept_homomorph:
qu[qu[...,0] < 0.0] *= -1
else:
@ -298,10 +355,21 @@ class Rotation:
return Rotation(qu)
@staticmethod
def from_Eulers(eulers,
def from_Eulers(phi,
degrees = False):
"""
Initialize from Bunge-Euler angles.
eu = np.array(eulers,dtype=float)
Parameters
----------
phi : numpy.ndarray of shape (...,3)
Bunge-Euler angles: (φ_1, ϕ, φ_2), φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]
unless degrees == True: φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360].
degrees : boolean, optional
Bunge-Euler angles are given in degrees. Defaults to False.
"""
eu = np.array(phi,dtype=float)
if eu.shape[:-2:-1] != (3,):
raise ValueError('Invalid shape.')
@ -316,12 +384,29 @@ class Rotation:
degrees = False,
normalise = False,
P = -1):
"""
Initialize from Axis angle pair.
Parameters
----------
axis_angle : numpy.ndarray of shape (...,4)
Axis angle pair: [n_1, n_2, n_3, ω], |n| = 1 and ω ∈ [0,π]
unless degrees = True: ω ∈ [0,180].
degrees : boolean, optional
Angle ω is given in degrees. Defaults to False.
normalize: boolean, optional
Allow |n| ≠ 1. Defaults to False.
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
ax = np.array(axis_angle,dtype=float)
if ax.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if P > 0: ax[...,0:3] *= -1 # convert from P=1 to P=-1
if P == 1: ax[...,0:3] *= -1
if degrees: ax[..., 3] = np.radians(ax[...,3])
if normalise: ax[...,0:3] /= np.linalg.norm(ax[...,0:3],axis=-1)
if np.any(ax[...,3] < 0.0) or np.any(ax[...,3] > np.pi):
@ -335,7 +420,19 @@ class Rotation:
def from_basis(basis,
orthonormal = True,
reciprocal = False):
"""
Initialize from lattice basis vectors.
Parameters
----------
basis : numpy.ndarray of shape (...,3,3)
Three lattice basis vectors in three dimensions.
orthonormal : boolean, optional
Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
reciprocal : boolean, optional
Basis vectors are given in reciprocal (instead of real) space. Defaults to False.
"""
om = np.array(basis,dtype=float)
if om.shape[:-3:-1] != (3,3):
raise ValueError('Invalid shape.')
@ -356,20 +453,43 @@ class Rotation:
return Rotation(Rotation._om2qu(om))
@staticmethod
def from_matrix(om):
def from_matrix(R):
"""
Initialize from rotation matrix.
return Rotation.from_basis(om)
Parameters
----------
R : numpy.ndarray of shape (...,3,3)
Rotation matrix: det(R) = 1, R.T∙R=I.
"""
return Rotation.from_basis(R)
@staticmethod
def from_Rodrigues(rodrigues,
def from_Rodrigues(rho,
normalise = False,
P = -1):
"""
Initialize from Rodrigues-Frank vector.
ro = np.array(rodrigues,dtype=float)
Parameters
----------
rho : numpy.ndarray of shape (...,4)
Rodrigues-Frank vector (angle separated from axis).
(n_1, n_2, n_3, tan(ω/2)), |n| = 1 and ω ∈ [0,π].
normalize : boolean, optional
Allow |n| ≠ 1. Defaults to False.
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
ro = np.array(rho,dtype=float)
if ro.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if P > 0: ro[...,0:3] *= -1 # convert from P=1 to P=-1
if P == 1: ro[...,0:3] *= -1
if normalise: ro[...,0:3] /= np.linalg.norm(ro[...,0:3],axis=-1)
if np.any(ro[...,3] < 0.0):
raise ValueError('Rodrigues vector rotation angle not positive.')
@ -379,14 +499,26 @@ class Rotation:
return Rotation(Rotation._ro2qu(ro))
@staticmethod
def from_homochoric(homochoric,
def from_homochoric(h,
P = -1):
"""
Initialize from homochoric vector.
ho = np.array(homochoric,dtype=float)
Parameters
----------
h : numpy.ndarray of shape (...,3)
Homochoric vector: (h_1, h_2, h_3), |h| < (3/4*π)^(1/3).
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
ho = np.array(h,dtype=float)
if ho.shape[:-2:-1] != (3,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if P > 0: ho *= -1 # convert from P=1 to P=-1
if P == 1: ho *= -1
if np.any(np.linalg.norm(ho,axis=-1) >_R1+1e-9):
raise ValueError('Homochoric coordinate outside of the sphere.')
@ -394,18 +526,30 @@ class Rotation:
return Rotation(Rotation._ho2qu(ho))
@staticmethod
def from_cubochoric(cubochoric,
P = -1):
def from_cubochoric(c,
P = -1):
"""
Initialize from cubochoric vector.
cu = np.array(cubochoric,dtype=float)
Parameters
----------
c : numpy.ndarray of shape (...,3)
Cubochoric vector: (c_1, c_2, c_3), max(c_i) < 1/2*π^(2/3).
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
cu = np.array(c,dtype=float)
if cu.shape[:-2:-1] != (3,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if np.abs(np.max(cu))>np.pi**(2./3.) * 0.5+1e-9:
raise ValueError('Cubochoric coordinate outside of the cube: {} {} {}.'.format(*cu))
if np.abs(np.max(cu)) > np.pi**(2./3.) * 0.5+1e-9:
raise ValueError('Cubochoric coordinate outside of the cube.')
ho = Rotation._cu2ho(cu)
if P > 0: ho *= -1 # convert from P=1 to P=-1
if P == 1: ho *= -1
return Rotation(Rotation._ho2qu(ho))
@ -458,7 +602,7 @@ class Rotation:
np.cos(2.0*np.pi*r[...,1])*B,
np.sin(2.0*np.pi*r[...,0])*A],axis=-1)
return Rotation(q.reshape(r.shape[:-1]+(4,)) if shape is not None else q).standardize()
return Rotation(q.reshape(r.shape[:-1]+(4,)) if shape is not None else q)._standardize()
# for compatibility (old names do not follow convention)
@ -471,7 +615,7 @@ class Rotation:
####################################################################################################
# Code below available according to the following conditions on https://github.com/MarDiehl/3Drotations
####################################################################################################
# Copyright (c) 2017-2019, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
# Copyright (c) 2017-2020, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
# Copyright (c) 2013-2014, Marc De Graef/Carnegie Mellon University
# All rights reserved.
#
@ -530,7 +674,7 @@ class Rotation:
np.zeros(qu.shape[:-1]+(2,))]),
np.where(np.abs(q03_s) < 1.0e-8,
np.block([np.arctan2( 2.0*qu[...,1:2]*qu[...,2:3],qu[...,1:2]**2-qu[...,2:3]**2),
np.broadcast_to(np.pi,qu.shape[:-1]+(1,)),
np.broadcast_to(np.pi,qu[...,0:1].shape),
np.zeros(qu.shape[:-1]+(1,))]),
np.block([np.arctan2((-_P*q02+q13)*chi, (-_P*q01-q23)*chi),
np.arctan2( 2.0*chi, q03_s-q12_s ),
@ -553,7 +697,7 @@ class Rotation:
s = np.sign(qu[...,0:1])/np.sqrt(qu[...,1:2]**2+qu[...,2:3]**2+qu[...,3:4]**2)
omega = 2.0 * np.arccos(np.clip(qu[...,0:1],-1.0,1.0))
ax = np.where(np.broadcast_to(qu[...,0:1] < 1.0e-8,qu.shape),
np.block([qu[...,1:4],np.broadcast_to(np.pi,qu.shape[:-1]+(1,))]),
np.block([qu[...,1:4],np.broadcast_to(np.pi,qu[...,0:1].shape)]),
np.block([qu[...,1:4]*s,omega]))
ax[np.isclose(qu[...,0],1.,rtol=0.0)] = [0.0, 0.0, 1.0, 0.0]
return ax
@ -564,7 +708,7 @@ class Rotation:
with np.errstate(invalid='ignore',divide='ignore'):
s = np.linalg.norm(qu[...,1:4],axis=-1,keepdims=True)
ro = np.where(np.broadcast_to(np.abs(qu[...,0:1]) < 1.0e-12,qu.shape),
np.block([qu[...,1:2], qu[...,2:3], qu[...,3:4], np.broadcast_to(np.inf,qu.shape[:-1]+(1,))]),
np.block([qu[...,1:2], qu[...,2:3], qu[...,3:4], np.broadcast_to(np.inf,qu[...,0:1].shape)]),
np.block([qu[...,1:2]/s,qu[...,2:3]/s,qu[...,3:4]/s,
np.tan(np.arccos(np.clip(qu[...,0:1],-1.0,1.0)))
])

12
python/damask/_vtk.py
View File

@ -1,4 +1,4 @@
import os
from pathlib import Path
import pandas as pd
import numpy as np
@ -126,8 +126,8 @@ class VTK:
vtkUnstructuredGrid, and vtkPolyData.
"""
ext = os.path.splitext(fname)[1]
if ext == '.vtk':
ext = Path(fname).suffix
if ext == '.vtk' or dataset_type:
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(fname)
reader.Update()
@ -176,10 +176,10 @@ class VTK:
writer = vtk.vtkXMLPolyDataWriter()
default_ext = writer.GetDefaultFileExtension()
name, ext = os.path.splitext(fname)
ext = Path(fname).suffix
if ext and ext != '.'+default_ext:
raise ValueError('Given extension {} is not .{}'.format(ext,default_ext))
writer.SetFileName('{}.{}'.format(name,default_ext))
raise ValueError('Given extension {} does not match default .{}'.format(ext,default_ext))
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
writer.SetInputData(self.geom)

36
python/damask/solver/_marc.py
View File

@ -1,7 +1,7 @@
import os
import subprocess
import shlex
import string
from pathlib import Path
from .._environment import Environment
@ -19,28 +19,24 @@ class Marc:
"""
self.solver = 'Marc'
try:
self.version = int(version)
except TypeError:
self.version = -1
self.version = version
#--------------------------
def libraryPath(self):
@property
def library_path(self):
path_MSC = Environment().options['MSC_ROOT']
path_lib = '{}/mentat{}/shlib/linux64'.format(path_MSC,self.version)
path_lib = Path('{}/mentat{}/shlib/linux64'.format(path_MSC,self.version))
return path_lib if os.path.exists(path_lib) else ''
return path_lib if path_lib.is_dir() else None
#--------------------------
def toolsPath(self):
@property
def tools_path(self):
path_MSC = Environment().options['MSC_ROOT']
path_tools = '{}/marc{}/tools'.format(path_MSC,self.version)
path_tools = Path('{}/marc{}/tools'.format(path_MSC,self.version))
return path_tools if os.path.exists(path_tools) else ''
return path_tools if path_tools.is_dir() else None
#--------------------------
@ -53,21 +49,21 @@ class Marc:
):
damaskEnv = Environment()
env = Environment()
user = os.path.join(damaskEnv.relPath('src'),'DAMASK_marc{}.{}'.format(self.version,'f90' if compile else 'marc'))
if not os.path.isfile(user):
user = env.root_dir/Path('src/DAMASK_marc{}'.format(self.version)).with_suffix('.f90' if compile else '.marc')
if not user.is_file():
raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),user))
# Define options [see Marc Installation and Operation Guide, pp 23]
script = 'run_damask_{}mp'.format(optimization)
cmd = os.path.join(self.toolsPath(),script) + \
cmd = str(self.tools_path/Path(script)) + \
' -jid ' + model + '_' + job + \
' -nprocd 1 -autorst 0 -ci n -cr n -dcoup 0 -b no -v no'
if compile: cmd += ' -u ' + user + ' -save y'
else: cmd += ' -prog ' + os.path.splitext(user)[0]
if compile: cmd += ' -u ' + str(user) + ' -save y'
else: cmd += ' -prog ' + str(user.with_suffix(''))
print('job submission {} compilation: {}'.format('with' if compile else 'without',user))
if logfile: log = open(logfile, 'w')

16
python/damask/util.py
View File

@ -27,7 +27,7 @@ __all__=[
####################################################################################################
def srepr(arg,glue = '\n'):
r"""
Join arguments as individual lines.
Join arguments with glue string.
Parameters
----------
@ -93,7 +93,7 @@ def strikeout(what):
def execute(cmd,
streamIn = None,
stream_in = None,
wd = './',
env = None):
"""
@ -103,7 +103,7 @@ def execute(cmd,
----------
cmd : str
Command to be executed.
streanIn :, optional
stream_in : file object, optional
Input (via pipe) for executed process.
wd : str, optional
Working directory of process. Defaults to ./ .
@ -119,14 +119,14 @@ def execute(cmd,
stderr = subprocess.PIPE,
stdin = subprocess.PIPE,
env = myEnv)
out,error = [i for i in (process.communicate() if streamIn is None
else process.communicate(streamIn.read().encode('utf-8')))]
stdout, stderr = [i for i in (process.communicate() if stream_in is None
else process.communicate(stream_in.read().encode('utf-8')))]
os.chdir(initialPath)
out = out.decode('utf-8').replace('\x08','')
error = error.decode('utf-8').replace('\x08','')
stdout = stdout.decode('utf-8').replace('\x08','')
stderr = stderr.decode('utf-8').replace('\x08','')
if process.returncode != 0:
raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
return out,error
return stdout, stderr
def show_progress(iterable,N_iter=None,prefix='',bar_length=50):

2
python/tests/test_Result.py
View File

@ -302,8 +302,8 @@ class TestResult:
@pytest.mark.parametrize('allowed',['off','on'])
def test_rename(self,default,allowed):
F = default.read_dataset(default.get_dataset_location('F'))
if allowed == 'on':
F = default.read_dataset(default.get_dataset_location('F'))
default.allow_modification()
default.rename('F','new_name')
assert np.all(F == default.read_dataset(default.get_dataset_location('new_name')))

36
python/tests/test_Rotation.py
View File

@ -14,7 +14,7 @@ scatter=1.e-2
@pytest.fixture
def default():
"""A set of n random rotations."""
"""A set of n rotations (corner cases and random)."""
specials = np.array([
[1.0, 0.0, 0.0, 0.0],
#----------------------
@ -170,7 +170,7 @@ def qu2ax(qu):
Modified version of the original formulation, should be numerically more stable
"""
if np.isclose(qu[0],1.,rtol=0.0): # set axis to [001] if the angle is 0/360
if np.isclose(qu[0],1.,rtol=0.0): # set axis to [001] if the angle is 0/360
ax = np.array([ 0.0, 0.0, 1.0, 0.0 ])
elif qu[0] > 1.e-8:
s = np.sign(qu[0])/np.sqrt(qu[1]**2+qu[2]**2+qu[3]**2)
@ -534,7 +534,7 @@ def mul(me, other):
other_p = other.quaternion[1:]
R = me.__class__(np.append(me_q*other_q - np.dot(me_p,other_p),
me_q*other_p + other_q*me_p + _P * np.cross(me_p,other_p)))
return R.standardize()
return R._standardize()
elif isinstance(other, np.ndarray):
if other.shape == (3,):
A = me.quaternion[0]**2.0 - np.dot(me.quaternion[1:],me.quaternion[1:])
@ -554,7 +554,7 @@ def mul(me, other):
axes = ((0, 2, 4, 6), (0, 1, 2, 3))
return np.tensordot(RRRR, other, axes)
else:
raise ValueError('Can only rotate vectors, 2nd order ternsors, and 4th order tensors')
raise ValueError('Can only rotate vectors, 2nd order tensors, and 4th order tensors')
else:
raise TypeError('Cannot rotate {}'.format(type(other)))
@ -854,6 +854,10 @@ class TestRotation:
rot = Rotation.from_basis(om,False,reciprocal=reciprocal)
assert np.isclose(np.linalg.det(rot.as_matrix()),1.0)
@pytest.mark.parametrize('shape',[None,1,(4,4)])
def test_random(self,shape):
Rotation.from_random(shape)
@pytest.mark.parametrize('function',[Rotation.from_quaternion,
Rotation.from_Eulers,
Rotation.from_axis_angle,
@ -866,6 +870,16 @@ class TestRotation:
with pytest.raises(ValueError):
function(invalid_shape)
@pytest.mark.parametrize('fr,to',[(Rotation.from_quaternion,'as_quaternion'),
(Rotation.from_axis_angle,'as_axis_angle'),
(Rotation.from_Rodrigues, 'as_Rodrigues'),
(Rotation.from_homochoric,'as_homochoric'),
(Rotation.from_cubochoric,'as_cubochoric')])
def test_invalid_P(self,fr,to):
R = Rotation.from_random(np.random.randint(8,32,(3))) # noqa
with pytest.raises(ValueError):
fr(eval('R.{}()'.format(to)),P=-30)
@pytest.mark.parametrize('shape',[None,(3,),(4,2)])
def test_broadcast(self,shape):
rot = Rotation.from_random(shape)
@ -932,14 +946,18 @@ class TestRotation:
phi_2 = 2*np.pi - phi_1
R_1 = Rotation.from_Eulers(np.array([phi_1,0.,0.]))
R_2 = Rotation.from_Eulers(np.array([0.,0.,phi_2]))
assert np.allclose(data,R_2*(R_1*data))
assert np.allclose(data,R_2@(R_1@data))
def test_rotate_inverse(self):
R = Rotation.from_random()
assert np.allclose(np.eye(3),(~R@R).as_matrix())
@pytest.mark.parametrize('data',[np.random.rand(3),
np.random.rand(3,3),
np.random.rand(3,3,3,3)])
def test_rotate_inverse(self,data):
def test_rotate_inverse_array(self,data):
R = Rotation.from_random()
assert np.allclose(data,R.inversed()*(R*data))
assert np.allclose(data,~R@(R@data))
@pytest.mark.parametrize('data',[np.random.rand(4),
np.random.rand(3,2),
@ -956,3 +974,7 @@ class TestRotation:
R = Rotation.from_random()
with pytest.raises(TypeError):
R*data
def test_misorientation(self):
R = Rotation.from_random()
assert np.allclose(R.misorientation(R).as_matrix(),np.eye(3))

34
python/tests/test_VTK.py
View File

@ -17,18 +17,24 @@ class TestVTK:
size = np.random.random(3) + 1.0
origin = np.random.random(3)
v = VTK.from_rectilinearGrid(grid,size,origin)
s = v.__repr__()
string = v.__repr__()
v.write(os.path.join(tmp_path,'rectilinearGrid'))
v = VTK.from_file(os.path.join(tmp_path,'rectilinearGrid.vtr'))
assert(s == v.__repr__())
vtr = VTK.from_file(os.path.join(tmp_path,'rectilinearGrid.vtr'))
with open(os.path.join(tmp_path,'rectilinearGrid.vtk'),'w') as f:
f.write(string)
vtk = VTK.from_file(os.path.join(tmp_path,'rectilinearGrid.vtk'),'VTK_rectilinearGrid')
assert(string == vtr.__repr__() == vtk.__repr__())
def test_polyData(self,tmp_path):
points = np.random.rand(3,100)
v = VTK.from_polyData(points)
s = v.__repr__()
string = v.__repr__()
v.write(os.path.join(tmp_path,'polyData'))
v = VTK.from_file(os.path.join(tmp_path,'polyData.vtp'))
assert(s == v.__repr__())
vtp = VTK.from_file(os.path.join(tmp_path,'polyData.vtp'))
with open(os.path.join(tmp_path,'polyData.vtk'),'w') as f:
f.write(string)
vtk = VTK.from_file(os.path.join(tmp_path,'polyData.vtk'),'polyData')
assert(string == vtp.__repr__() == vtk.__repr__())
@pytest.mark.parametrize('cell_type,n',[
('VTK_hexahedron',8),
@ -41,7 +47,17 @@ class TestVTK:
nodes = np.random.rand(n,3)
connectivity = np.random.choice(np.arange(n),n,False).reshape(-1,n)
v = VTK.from_unstructuredGrid(nodes,connectivity,cell_type)
s = v.__repr__()
string = v.__repr__()
v.write(os.path.join(tmp_path,'unstructuredGrid'))
v = VTK.from_file(os.path.join(tmp_path,'unstructuredGrid.vtu'))
assert(s == v.__repr__())
vtu = VTK.from_file(os.path.join(tmp_path,'unstructuredGrid.vtu'))
with open(os.path.join(tmp_path,'unstructuredGrid.vtk'),'w') as f:
f.write(string)
vtk = VTK.from_file(os.path.join(tmp_path,'unstructuredGrid.vtk'),'unstructuredgrid')
assert(string == vtu.__repr__() == vtk.__repr__())
@pytest.mark.parametrize('name,dataset_type',[('this_file_does_not_exist.vtk',None),
('this_file_does_not_exist.vtk','vtk'),
('this_file_does_not_exist.vtx', None)])
def test_invalid_dataset_type(self,dataset_type,name):
with pytest.raises(TypeError):
VTK.from_file('this_file_does_not_exist.vtk',dataset_type)

11
python/tests/test_util.py Normal file
View File

@ -0,0 +1,11 @@
from damask import util
class TestUtil:
def test_execute_direct(self):
out,err = util.execute('echo test')
assert out=='test\n' and err==''
def test_execute_env(self):
out,err = util.execute('sh -c "echo $test_for_execute"',env={'test_for_execute':'test'})
assert out=='test\n' and err==''

12
src/IO.f90
View File

@ -11,7 +11,6 @@ module IO
implicit none
private
character(len=*), parameter, public :: &
IO_EOF = '#EOF#', & !< end of file string
IO_WHITESPACE = achar(44)//achar(32)//achar(9)//achar(10)//achar(13) !< whitespace characters
character, parameter, public :: &
IO_EOL = new_line('DAMASK'), & !< end of line character
@ -106,7 +105,7 @@ function IO_readlines(fileName) result(fileContent)
endif
startPos = endPos + 2 ! jump to next line start
fileContent(l) = line
fileContent(l) = trim(line)//''
l = l + 1
enddo
@ -114,7 +113,8 @@ end function IO_readlines
!--------------------------------------------------------------------------------------------------
!> @brief reads an entire ASCII file into a string
!> @brief read ASCII file into a string
!> @details ensures that the string ends with a new line (expected UNIX behavior)
!--------------------------------------------------------------------------------------------------
function IO_read(fileName) result(fileContent)
@ -130,10 +130,14 @@ function IO_read(fileName) result(fileContent)
status='old', position='rewind', action='read',iostat=myStat)
if(myStat /= 0) call IO_error(100,ext_msg=trim(fileName))
allocate(character(len=fileLength)::fileContent)
if(fileLength==0) return
read(fileUnit,iostat=myStat) fileContent
if(myStat > 0) call IO_error(102,ext_msg=trim(fileName)) ! <0 for ifort (https://software.intel.com/en-us/comment/1960081)
if(myStat /= 0) call IO_error(102,ext_msg=trim(fileName))
close(fileUnit)
if(fileContent(fileLength:fileLength) /= IO_EOL) fileContent = fileContent//IO_EOL ! ensure EOL@EOF
end function IO_read

2
src/constitutive_plastic_dislotwin.f90
View File

@ -830,7 +830,7 @@ module subroutine plastic_dislotwin_results(instance,group)
'mobile dislocation density','1/m²')
case('rho_dip')
if(prm%sum_N_sl>0) call results_writeDataset(group,stt%rho_dip,'rho_dip',&
'dislocation dipole density''1/m²')
'dislocation dipole density','1/m²')
case('gamma_sl')
if(prm%sum_N_sl>0) call results_writeDataset(group,stt%gamma_sl,'gamma_sl',&
'plastic shear','1')

4
src/crystallite.f90
View File

@ -284,11 +284,9 @@ end subroutine crystallite_init
!--------------------------------------------------------------------------------------------------
!> @brief calculate stress (P)
!--------------------------------------------------------------------------------------------------
function crystallite_stress(dummyArgumentToPreventInternalCompilerErrorWithGCC)
function crystallite_stress()
logical, dimension(discretization_nIP,discretization_nElem) :: crystallite_stress
real(pReal), intent(in), optional :: &
dummyArgumentToPreventInternalCompilerErrorWithGCC
real(pReal) :: &
formerSubStep
integer :: &

2
src/discretization.f90
View File

@ -49,7 +49,7 @@ subroutine discretization_init(homogenizationAt,microstructureAt,&
IPcoords0, &
NodeCoords0
integer, optional, intent(in) :: &
sharedNodesBegin
sharedNodesBegin !< index of first node shared among different processes (MPI)
write(6,'(/,a)') ' <<<+- discretization init -+>>>'; flush(6)

1
src/grid/DAMASK_grid.f90
View File

@ -321,7 +321,6 @@ program DAMASK_grid
loadCases = [loadCases,newLoadCase] ! load case is ok, append it
enddo
!--------------------------------------------------------------------------------------------------
! doing initialization depending on active solvers
call spectral_Utilities_init

166
src/mesh/discretization_mesh.f90
View File

@ -8,54 +8,50 @@ module discretization_mesh
#include <petsc/finclude/petscdmplex.h>
#include <petsc/finclude/petscis.h>
#include <petsc/finclude/petscdmda.h>
use PETScdmplex
use PETScdmda
use PETScis
use PETScdmplex
use PETScdmda
use PETScis
use DAMASK_interface
use IO
use debug
use discretization
use numerics
use FEsolving
use FEM_quadrature
use prec
use YAML_types
implicit none
private
integer, public, protected :: &
mesh_Nboundaries, &
mesh_NcpElemsGlobal
use DAMASK_interface
use IO
use debug
use discretization
use numerics
use FEsolving
use FEM_quadrature
use prec
integer :: &
mesh_NcpElems !< total number of CP elements in mesh
implicit none
private
integer, public, protected :: &
mesh_Nboundaries, &
mesh_NcpElemsGlobal
integer :: &
mesh_NcpElems !< total number of CP elements in mesh
!!!! BEGIN DEPRECATED !!!!!
integer, public, protected :: &
mesh_maxNips !< max number of IPs in any CP element
integer, public, protected :: &
mesh_maxNips !< max number of IPs in any CP element
!!!! BEGIN DEPRECATED !!!!!
integer, dimension(:,:), allocatable :: &
mesh_element !DEPRECATED
real(pReal), dimension(:,:), allocatable :: &
mesh_ipVolume, & !< volume associated with IP (initially!)
mesh_node0 !< node x,y,z coordinates (initially!)
real(pReal), dimension(:,:), allocatable :: &
mesh_ipVolume, & !< volume associated with IP (initially!)
mesh_node0 !< node x,y,z coordinates (initially!)
real(pReal), dimension(:,:,:), allocatable :: &
mesh_ipCoordinates !< IP x,y,z coordinates (after deformation!)
real(pReal), dimension(:,:,:), allocatable :: &
mesh_ipCoordinates !< IP x,y,z coordinates (after deformation!)
DM, public :: geomMesh
PetscInt, dimension(:), allocatable, public, protected :: &
mesh_boundaries
DM, public :: geomMesh
public :: &
discretization_mesh_init, &
mesh_FEM_build_ipVolumes, &
mesh_FEM_build_ipCoordinates
PetscInt, dimension(:), allocatable, public, protected :: &
mesh_boundaries
public :: &
discretization_mesh_init, &
mesh_FEM_build_ipVolumes, &
mesh_FEM_build_ipCoordinates
contains
@ -68,46 +64,40 @@ subroutine discretization_mesh_init(restart)
logical, intent(in) :: restart
integer, dimension(1), parameter:: FE_geomtype = [1] !< geometry type of particular element type
integer, dimension(1) :: FE_Nips !< number of IPs in a specific type of element
integer, allocatable, dimension(:) :: chunkPos
integer :: dimPlex, &
mesh_Nnodes, & !< total number of nodes in mesh
j, l
integer, parameter :: &
mesh_ElemType=1 !< Element type of the mesh (only support homogeneous meshes)
PetscSF :: sf
DM :: globalMesh
PetscInt :: nFaceSets
PetscInt, pointer, dimension(:) :: pFaceSets
character(len=pStringLen), dimension(:), allocatable :: fileContent
IS :: faceSetIS
IS :: faceSetIS
PetscErrorCode :: ierr
integer, dimension(:), allocatable :: &
homogenizationAt, &
microstructureAt
class(tNode), pointer :: &
num_mesh
integer :: integrationOrder !< order of quadrature rule required
num_mesh => numerics_root%get('mesh',defaultVal=emptyDict)
integrationOrder = num_mesh%get_asInt('integrationorder',defaultVal = 2)
write(6,'(/,a)') ' <<<+- mesh init -+>>>'
! read in file
num_mesh => numerics_root%get('mesh',defaultVal=emptyDict)
integrationOrder = num_mesh%get_asInt('integrationorder',defaultVal = 2)
call DMPlexCreateFromFile(PETSC_COMM_WORLD,geometryFile,PETSC_TRUE,globalMesh,ierr)
CHKERRQ(ierr)
! get spatial dimension (2 or 3?)
call DMGetDimension(globalMesh,dimPlex,ierr)
CHKERRQ(ierr)
write(6,*) 'dimension',dimPlex;flush(6)
call DMGetStratumSize(globalMesh,'depth',dimPlex,mesh_NcpElemsGlobal,ierr)
CHKERRQ(ierr)
! get number of IDs in face sets (for boundary conditions?)
call DMGetLabelSize(globalMesh,'Face Sets',mesh_Nboundaries,ierr)
CHKERRQ(ierr)
write(6,*) 'number of "Face Sets"',mesh_Nboundaries;flush(6)
call MPI_Bcast(mesh_Nboundaries,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
call MPI_Bcast(mesh_NcpElemsGlobal,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
call MPI_Bcast(dimPlex,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
@ -127,7 +117,7 @@ subroutine discretization_mesh_init(restart)
call MPI_Bcast(mesh_boundaries,mesh_Nboundaries,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
if (worldrank == 0) then
fileContent = IO_read_ASCII(geometryFile)
fileContent = IO_readlines(geometryFile)
l = 0
do
l = l + 1
@ -150,48 +140,42 @@ subroutine discretization_mesh_init(restart)
enddo
call DMClone(globalMesh,geomMesh,ierr)
CHKERRQ(ierr)
else
else
call DMPlexDistribute(globalMesh,0,sf,geomMesh,ierr)
CHKERRQ(ierr)
endif
endif
call DMDestroy(globalMesh,ierr); CHKERRQ(ierr)
call DMGetStratumSize(geomMesh,'depth',dimPlex,mesh_NcpElems,ierr)
CHKERRQ(ierr)
call DMGetStratumSize(geomMesh,'depth',0,mesh_Nnodes,ierr)
CHKERRQ(ierr)
FE_Nips(FE_geomtype(1)) = FEM_nQuadrature(dimPlex,integrationOrder)
mesh_maxNips = FE_Nips(1)
write(6,*) 'mesh_maxNips',mesh_maxNips
mesh_maxNips = FEM_nQuadrature(dimPlex,integrationOrder)
call mesh_FEM_build_ipCoordinates(dimPlex,FEM_quadrature_points(dimPlex,integrationOrder)%p)
call mesh_FEM_build_ipVolumes(dimPlex)
allocate (mesh_element (4,mesh_NcpElems)); mesh_element = 0
do j = 1, mesh_NcpElems
mesh_element( 1,j) = -1 ! DEPRECATED
mesh_element( 2,j) = mesh_elemType ! elem type
mesh_element( 3,j) = 1 ! homogenization
call DMGetLabelValue(geomMesh,'material',j-1,mesh_element(4,j),ierr)
CHKERRQ(ierr)
end do
if (debug_e < 1 .or. debug_e > mesh_NcpElems) &
call IO_error(602,ext_msg='element') ! selected element does not exist
if (debug_i < 1 .or. debug_i > FE_Nips(FE_geomtype(mesh_element(2,debug_e)))) &
call IO_error(602,ext_msg='IP') ! selected element does not have requested IP
FEsolving_execElem = [ 1,mesh_NcpElems ] ! parallel loop bounds set to comprise all DAMASK elements
FEsolving_execIP = [1,FE_Nips(FE_geomtype(mesh_element(2,1)))]
allocate(microstructureAt(mesh_NcpElems))
allocate(homogenizationAt(mesh_NcpElems),source=1)
do j = 1, mesh_NcpElems
call DMGetLabelValue(geomMesh,'material',j-1,microstructureAt(j),ierr)
CHKERRQ(ierr)
end do
if (debug_e < 1 .or. debug_e > mesh_NcpElems) call IO_error(602,ext_msg='element')
if (debug_i < 1 .or. debug_i > mesh_maxNips) call IO_error(602,ext_msg='IP')
FEsolving_execElem = [1,mesh_NcpElems] ! parallel loop bounds set to comprise all DAMASK elements
FEsolving_execIP = [1,mesh_maxNips]
allocate(mesh_node0(3,mesh_Nnodes),source=0.0_pReal)
call discretization_init(mesh_element(3,:),mesh_element(4,:),&
call discretization_init(microstructureAt,homogenizationAt,&
reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &
mesh_node0)
end subroutine discretization_mesh_init
@ -199,23 +183,23 @@ end subroutine discretization_mesh_init
!> @brief Calculates IP volume. Allocates global array 'mesh_ipVolume'
!--------------------------------------------------------------------------------------------------
subroutine mesh_FEM_build_ipVolumes(dimPlex)
PetscInt,intent(in):: dimPlex
PetscReal :: vol
PetscReal, pointer,dimension(:) :: pCent, pNorm
PetscInt :: cellStart, cellEnd, cell
PetscErrorCode :: ierr
allocate(mesh_ipVolume(mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
allocate(pCent(dimPlex))
allocate(pNorm(dimPlex))
do cell = cellStart, cellEnd-1
call DMPlexComputeCellGeometryFVM(geomMesh,cell,vol,pCent,pNorm,ierr)
call DMPlexComputeCellGeometryFVM(geomMesh,cell,vol,pCent,pNorm,ierr)
CHKERRQ(ierr)
mesh_ipVolume(:,cell+1) = vol/real(mesh_maxNips,pReal)
enddo
enddo
end subroutine mesh_FEM_build_ipVolumes
@ -227,20 +211,20 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
PetscInt, intent(in) :: dimPlex
PetscReal, intent(in) :: qPoints(mesh_maxNips*dimPlex)
PetscReal, pointer,dimension(:) :: pV0, pCellJ, pInvcellJ
PetscReal :: detJ
PetscInt :: cellStart, cellEnd, cell, qPt, dirI, dirJ, qOffset
PetscErrorCode :: ierr
allocate(mesh_ipCoordinates(3,mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
allocate(pV0(dimPlex))
allocatE(pCellJ(dimPlex**2))
allocatE(pinvCellJ(dimPlex**2))
call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
do cell = cellStart, cellEnd-1 !< loop over all elements
do cell = cellStart, cellEnd-1 !< loop over all elements
call DMPlexComputeCellGeometryAffineFEM(geomMesh,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
CHKERRQ(ierr)
qOffset = 0
@ -254,7 +238,7 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
enddo
qOffset = qOffset + dimPlex
enddo
enddo
enddo
end subroutine mesh_FEM_build_ipCoordinates

2
src/quaternions.f90
View File

@ -101,6 +101,8 @@ module quaternions
assignment(=), &
conjg, aimag, &
log, exp, &
abs, dot_product, &
inverse, &
real
contains