Martin Diehl
parent
111a1a76c6
commit
be9e00347b
8
Makefile
8
Makefile
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@ -1,7 +1,9 @@
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SHELL = /bin/sh
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########################################################################################
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# Makefile for the installation of DAMASK
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########################################################################################
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###################################################################################################
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# One-command-build invoking CMake (meant for developers, should not be part of the distribution)
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###################################################################################################
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.PHONY: all
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all: grid mesh
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@ -39,20 +39,20 @@ class Colormap(mpl.colors.ListedColormap):
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"""
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def __add__(self,other):
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"""Concatenate colormaps."""
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"""Concatenate."""
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return Colormap(np.vstack((self.colors,other.colors)),
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f'{self.name}+{other.name}')
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def __iadd__(self,other):
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"""Concatenate colormaps."""
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"""Concatenate (in-place)."""
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return self.__add__(other)
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def __invert__(self):
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"""Return inverted colormap."""
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"""Reverse."""
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return self.reversed()
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def __repr__(self):
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"""Show colormap as matplotlib figure."""
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"""Show as matplotlib figure."""
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fig = plt.figure(self.name,figsize=(5,.5))
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ax1 = fig.add_axes([0, 0, 1, 1])
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ax1.set_axis_off()
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@ -207,7 +207,7 @@ class Colormap(mpl.colors.ListedColormap):
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def reversed(self,name=None):
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"""
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Make a reversed instance of the colormap.
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Reverse.
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Parameters
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----------
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@ -31,7 +31,7 @@ class NiceDumper(yaml.SafeDumper):
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return super().represent_data(data)
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def ignore_aliases(self, data):
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"""No references."""
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"""Do not use references to existing objects."""
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return True
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class Config(dict):
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@ -9,14 +9,29 @@ from . import Orientation
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from . import util
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class ConfigMaterial(Config):
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"""Material configuration."""
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"""
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Material configuration.
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Manipulate material configurations for storage in YAML format.
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A complete material configuration file has the entries 'material',
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'phase', and 'homogenization'. For use in DAMASK, it needs to be
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stored as 'material.yaml'.
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"""
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_defaults = {'material': [],
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'homogenization': {},
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'phase': {}}
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def __init__(self,d=_defaults):
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"""Initialize object with default dictionary keys."""
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"""
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New material configuration.
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Parameters
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----------
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d : dictionary, optional
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Initial content. Defaults to empty material, homogenization, and phase entries.
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"""
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super().__init__(d)
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@ -17,11 +17,18 @@ from . import Rotation
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class Grid:
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"""Geometry definition for grid solvers."""
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"""
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Geometry definition for grid solvers.
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Create and manipulate geometry definitions for storage as VTK
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rectiliear grid files ('.vtr' extension). A grid contains the
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material ID (referring to the entry in 'material.yaml') and
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the physical size.
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"""
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def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
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"""
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New grid definition from array of materials, size, and origin.
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New geometry definition for grid solvers.
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Parameters
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----------
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@ -47,19 +47,30 @@ class Orientation(Rotation):
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The Bravais lattice is one of Orientation.lattice_symmetries:
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- aP : triclinic primitive
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- mP : monoclinic primitive
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- mS : ... base-centered
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- oP : orthorhombic primitive
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- oS : ... base-centered
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- oI : ... body-centered
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- oF : ... face-centered
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- tP : tetragonal primitive
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- tI : ... body-centered
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- hP : hexagonal primitive
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- cP : cubic primitive
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- cI : ... body-centered
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- cF : ... face-centered
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- triclinic
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- aP : primitive
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- monoclininic
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- mP : primitive
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- mS : base-centered
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- orthorhombic
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- oP : primitive
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- oS : base-centered
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- oI : body-centered
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- oF : face-centered
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- tetragonal
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- tP : primitive
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- tI : body-centered
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- hexagonal
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- hP : primitive
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- cubic
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- cP : primitive
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- cI : body-centered
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- cF : face-centered
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and inherits the corresponding crystal family.
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Specifying a Bravais lattice, compared to just the crystal family,
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@ -111,7 +122,7 @@ class Orientation(Rotation):
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alpha = None,beta = None,gamma = None,
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degrees = False):
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"""
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Initialize orientation object.
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New orientation.
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Parameters
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----------
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@ -26,14 +26,14 @@ h5py3 = h5py.__version__[0] == '3'
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class Result:
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"""
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Read and write to DADF5 files.
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Manipulate and read DADF5 files.
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DADF5 (DAMASK HDF5) files contain DAMASK results.
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"""
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def __init__(self,fname):
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"""
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Open an existing DADF5 file.
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New result view bound to a HDF5 file.
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Parameters
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----------
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@ -51,7 +51,7 @@ class Rotation:
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def __init__(self,rotation = np.array([1.0,0.0,0.0,0.0])):
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"""
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Initialize rotation object.
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New rotation.
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Parameters
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----------
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@ -140,7 +140,7 @@ class Rotation:
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def __len__(self):
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"""Length of leading/leftmost dimension of Rotation array."""
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"""Length of leading/leftmost dimension of array."""
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return 0 if self.shape == () else self.shape[0]
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@ -180,7 +180,7 @@ class Rotation:
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def __mul__(self,other):
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"""
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Compose this rotation with other.
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Compose with other.
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Parameters
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----------
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@ -206,7 +206,7 @@ class Rotation:
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def __imul__(self,other):
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"""
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Compose this rotation with other (in-place).
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Compose with other (in-place).
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Parameters
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----------
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@ -219,7 +219,7 @@ class Rotation:
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def __truediv__(self,other):
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"""
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Compose this rotation with inverse of other.
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Compose with inverse of other.
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Parameters
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----------
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@ -239,7 +239,7 @@ class Rotation:
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def __itruediv__(self,other):
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"""
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Compose this rotation with inverse of other (in-place).
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Compose with inverse of other (in-place).
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Parameters
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----------
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@ -252,7 +252,7 @@ class Rotation:
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def __matmul__(self,other):
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"""
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Rotation of vector, second order tensor, or fourth order tensor.
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Rotate vector, second order tensor, or fourth order tensor.
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Parameters
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----------
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@ -301,7 +301,7 @@ class Rotation:
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def append(self,other):
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"""
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Extend rotation array along first dimension with other array(s).
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Extend array along first dimension with other array(s).
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Parameters
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----------
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@ -313,19 +313,19 @@ class Rotation:
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def flatten(self,order = 'C'):
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"""Flatten quaternion array."""
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"""Flatten array."""
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return self.copy(rotation=self.quaternion.reshape((-1,4),order=order))
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def reshape(self,shape,order = 'C'):
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"""Reshape quaternion array."""
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"""Reshape array."""
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if isinstance(shape,(int,np.integer)): shape = (shape,)
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return self.copy(rotation=self.quaternion.reshape(tuple(shape)+(4,),order=order))
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def broadcast_to(self,shape,mode = 'right'):
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"""
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Broadcast quaternion array to shape.
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Broadcast array.
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Parameters
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----------
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def average(self,weights = None):
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"""
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Average rotations along last dimension.
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Average along last array dimension.
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Parameters
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----------
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def misorientation(self,other):
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"""
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Calculate misorientation from self to other Rotation.
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Calculate misorientation to other Rotation.
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Parameters
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----------
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@ -7,7 +7,7 @@ import numpy as np
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from . import util
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class Table:
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"""Store spreadsheet-like data."""
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"""Manipulate multi-dimensional spreadsheet-like data."""
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def __init__(self,data,shapes,comments=None):
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"""
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"""
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Load from ASCII table file.
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In legacy style, the first line indicates the number of
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subsequent header lines as "N header", with the last header line being
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interpreted as column labels.
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Alternatively, initial comments are marked by '#', with the first non-comment line
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Initial comments are marked by '#', the first non-comment line
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containing the column labels.
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Vector data column labels are indicated by '1_v, 2_v, ..., n_v'.
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Tensor data column labels are indicated by '3x3:1_T, 3x3:2_T, ..., 3x3:9_T'.
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- Vector data column labels are indicated by '1_v, 2_v, ..., n_v'.
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- Tensor data column labels are indicated by '3x3:1_T, 3x3:2_T, ..., 3x3:9_T'.
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Parameters
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----------
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@ -97,14 +95,6 @@ class Table:
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f = fname
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f.seek(0)
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try:
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N_comment_lines,keyword = f.readline().strip().split(maxsplit=1)
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if keyword != 'header':
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raise ValueError
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else:
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comments = [f.readline().strip() for i in range(1,int(N_comment_lines))]
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labels = f.readline().split()
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except ValueError:
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f.seek(0)
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comments = []
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line = f.readline().strip()
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@ -391,7 +381,7 @@ class Table:
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return dup
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def save(self,fname,legacy=False):
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def save(self,fname):
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"""
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Save as plain text file.
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@ -399,9 +389,6 @@ class Table:
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----------
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fname : file, str, or pathlib.Path
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Filename or file for writing.
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legacy : Boolean, optional
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Write table in legacy style, indicating header lines by "N header"
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in contrast to using comment sign ('#') at beginning of lines.
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"""
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seen = set()
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labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
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for i in range(np.prod(self.shapes[l]))]
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header = ([f'{len(self.comments)+1} header'] + self.comments) if legacy else \
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[f'# {comment}' for comment in self.comments]
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try:
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fhandle = open(fname,'w',newline='\n')
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except TypeError:
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fhandle = fname
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for line in header + [' '.join(labels)]: fhandle.write(line+'\n')
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fhandle.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+'\n')
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self.data.to_csv(fhandle,sep=' ',na_rep='nan',index=False,header=False)
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def __init__(self,vtk_data):
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"""
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Initialize from vtk dataset.
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New spatial visualization.
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Parameters
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----------
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@ -155,7 +155,9 @@ def scale_to_coprime(v):
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def lcm(a,b):
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"""Least common multiple."""
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# Python 3.9 provides math.lcm, see https://stackoverflow.com/questions/51716916.
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try:
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return np.lcm(a,b) # numpy > 1.18
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except AttributeError:
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return a * b // np.gcd(a, b)
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m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
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@ -405,7 +407,7 @@ class return_message:
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def __init__(self,message):
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"""
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Sets return message.
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Set return message.
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Parameters
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----------
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@ -429,7 +431,7 @@ class _ProgressBar:
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def __init__(self,total,prefix,bar_length):
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"""
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Inititalize a progress bar to current time as basis for ETA estimation.
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Set current time as basis for ETA estimation.
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Parameters
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----------
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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180.0 45.00000000000001 180.0 1 1
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270.0 45.00000000000001 90.0 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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146.75362934444064 9.976439066337804 256.395594327347 1 1
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356.59977719102034 43.39784965440254 12.173896584899929 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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166.39559432734697 9.976439066337804 236.75362934444058 1 1
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352.1156357053931 43.82007387041961 14.074783631236542 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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114.20342833932975 10.52877936550932 204.20342833932972 1 1
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94.3573968784815 80.40593177313954 311.22729452432543 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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96.91733794010702 83.13253115922213 314.5844440567886 1 1
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173.082662059893 83.13253115922211 45.41555594321143 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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135.41555594321144 83.13253115922213 173.082662059893 1 1
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260.26438968275465 90.0 135.0 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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0.0 45.00000000000001 0.0 1 1
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90.0 45.00000000000001 270.0 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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283.60440567265294 9.976439066337804 33.24637065555936 1 1
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167.8261034151001 43.397849654402556 183.40022280897963 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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303.24637065555936 9.976439066337804 13.604405672652977 1 1
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165.92521636876344 43.82007387041961 187.88436429460683 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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335.7965716606702 10.528779365509317 65.79657166067024 1 1
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228.77270547567446 80.40593177313953 85.64260312151849 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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225.41555594321144 83.13253115922213 83.08266205989301 1 1
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134.58444405678856 83.13253115922211 6.917337940107012 1 2
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@ -1,4 +1,3 @@
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1 header
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1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
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6.9173379401070045 83.13253115922213 44.58444405678856 1 1
|
||||
45.0 89.99999999999999 279.7356103172453 1 2
|
||||
|
|
|
|||
|
|
@ -60,13 +60,6 @@ class TestTable:
|
|||
new = Table.load(f)
|
||||
assert all(default.data==new.data) and default.shapes == new.shapes
|
||||
|
||||
def test_write_read_legacy_style(self,default,tmp_path):
|
||||
with open(tmp_path/'legacy.txt','w') as f:
|
||||
default.save(f,legacy=True)
|
||||
with open(tmp_path/'legacy.txt') as f:
|
||||
new = Table.load(f)
|
||||
assert all(default.data==new.data) and default.shapes == new.shapes
|
||||
|
||||
def test_write_invalid_format(self,default,tmp_path):
|
||||
with pytest.raises(TypeError):
|
||||
default.save(tmp_path/'shouldnotbethere.txt',format='invalid')
|
||||
|
|
|
|||
Loading…
Reference in New Issue