512 lines
18 KiB
Python
512 lines
18 KiB
Python
import numpy as np
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import h5py
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from typing import Sequence, Dict, Any, Collection
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from ._typehints import FileHandle
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from . import Config
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from . import Rotation
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from . import Orientation
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from . import util
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from . import Table
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class ConfigMaterial(Config):
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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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def __init__(self,
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d: Dict[str, Any] = None,
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**kwargs):
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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 or YAML string, optional
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Initial content. Defaults to None, in which case empty entries for
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any missing material, homogenization, and phase entry are created.
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kwargs : key=value pairs, optional
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Initial content specified as pairs of key=value.
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"""
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default: Collection
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if d is None:
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for section, default in {'material':[],'homogenization':{},'phase':{}}.items():
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if section not in kwargs: kwargs.update({section:default})
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super().__init__(d,**kwargs)
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def save(self,
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fname: FileHandle = 'material.yaml',
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**kwargs):
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"""
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Save to yaml file.
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Parameters
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----------
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fname : file, str, or pathlib.Path, optional
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Filename or file for writing. Defaults to 'material.yaml'.
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**kwargs
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Keyword arguments parsed to yaml.dump.
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"""
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super().save(fname,**kwargs)
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@classmethod
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def load(cls,
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fname: FileHandle = 'material.yaml') -> 'ConfigMaterial':
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"""
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Load from yaml file.
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Parameters
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----------
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fname : file, str, or pathlib.Path, optional
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Filename or file to read from. Defaults to 'material.yaml'.
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Returns
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-------
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loaded : damask.ConfigMaterial
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Material configuration from file.
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"""
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return super(ConfigMaterial,cls).load(fname)
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@staticmethod
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def load_DREAM3D(fname: str,
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grain_data: str = None,
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cell_data: str = None,
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cell_ensemble_data: str = 'CellEnsembleData',
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phases: str = 'Phases',
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Euler_angles: str = 'EulerAngles',
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phase_names: str = 'PhaseName',
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base_group: str = None) -> 'ConfigMaterial':
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"""
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Load DREAM.3D (HDF5) file.
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Data in DREAM.3D files can be stored per cell ('CellData')
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and/or per grain ('Grain Data'). Per default, cell-wise data
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is assumed.
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damask.Grid.load_DREAM3D allows to get the corresponding geometry
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for the grid solver.
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Parameters
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----------
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fname : str
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Filename of the DREAM.3D (HDF5) file.
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grain_data : str
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Name of the group (folder) containing grain-wise data. Defaults
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to None, in which case cell-wise data is used.
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cell_data : str
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Name of the group (folder) containing cell-wise data. Defaults to
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None in wich case it is automatically detected.
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cell_ensemble_data : str
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Name of the group (folder) containing data of cell ensembles. This
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group is used to inquire the name of the phases. Phases will get
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numeric IDs if this group is not found. Defaults to 'CellEnsembleData'.
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phases : str
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Name of the dataset containing the phase ID (cell-wise or grain-wise).
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Defaults to 'Phases'.
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Euler_angles : str
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Name of the dataset containing the crystallographic orientation as
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Euler angles in radians (cell-wise or grain-wise). Defaults to 'EulerAngles'.
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phase_names : str
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Name of the dataset containing the phase names. Phases will get
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numeric IDs if this dataset is not found. Defaults to 'PhaseName'.
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base_group : str
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Path to the group (folder) that contains geometry (_SIMPL_GEOMETRY),
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and grain- or cell-wise data. Defaults to None, in which case
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it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
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Notes
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-----
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Homogenization and phase entries are emtpy and need to be defined separately.
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Returns
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-------
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loaded : damask.ConfigMaterial
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Material configuration from file.
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"""
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b = util.DREAM3D_base_group(fname) if base_group is None else base_group
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c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
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f = h5py.File(fname,'r')
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if grain_data is None:
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phase = f['/'.join([b,c,phases])][()].flatten()
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O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
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_,idx = np.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0)
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idx = np.sort(idx)
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else:
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phase = f['/'.join([b,grain_data,phases])][()]
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O = Rotation.from_Euler_angles(f['/'.join([b,grain_data,Euler_angles])]).as_quaternion() # noqa
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idx = np.arange(phase.size)
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if cell_ensemble_data is not None and phase_names is not None:
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try:
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names = np.array([s.decode() for s in f['/'.join([b,cell_ensemble_data,phase_names])]])
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phase = names[phase]
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except KeyError:
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pass
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base_config = ConfigMaterial({'phase':{k if isinstance(k,int) else str(k):'t.b.d.' for k in np.unique(phase)},
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'homogenization':{'direct':{'N_constituents':1}}})
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constituent = {k:np.atleast_1d(v[idx].squeeze()) for k,v in zip(['O','phase'],[O,phase])}
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return base_config.material_add(**constituent,homogenization='direct')
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@staticmethod
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def from_table(table: Table,
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**kwargs) -> 'ConfigMaterial':
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"""
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Generate from an ASCII table.
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Parameters
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----------
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table : damask.Table
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Table that contains material information.
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**kwargs
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Keyword arguments where the key is the property name and
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the value specifies either the label of the data column in the table
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or a constant value.
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Returns
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-------
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new : damask.ConfigMaterial
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Material configuration from values in table.
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Examples
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--------
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>>> import damask
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>>> import damask.ConfigMaterial as cm
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>>> t = damask.Table.load('small.txt')
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>>> t
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pos pos pos qu qu qu qu phase homog
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0 0 0 0 0.19 0.8 0.24 -0.51 Aluminum SX
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1 1 0 0 0.8 0.19 0.24 -0.51 Steel SX
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1 1 1 0 0.8 0.19 0.24 -0.51 Steel SX
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>>> cm.from_table(t,O='qu',phase='phase',homogenization='homog')
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material:
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- constituents:
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- O: [0.19, 0.8, 0.24, -0.51]
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v: 1.0
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phase: Aluminum
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homogenization: SX
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- constituents:
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- O: [0.8, 0.19, 0.24, -0.51]
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v: 1.0
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phase: Steel
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homogenization: SX
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homogenization: {}
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phase: {}
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>>> cm.from_table(t,O='qu',phase='phase',homogenization='single_crystal')
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material:
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- constituents:
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- O: [0.19, 0.8, 0.24, -0.51]
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v: 1.0
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phase: Aluminum
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homogenization: single_crystal
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- constituents:
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- O: [0.8, 0.19, 0.24, -0.51]
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v: 1.0
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phase: Steel
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homogenization: single_crystal
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homogenization: {}
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phase: {}
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"""
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kwargs_ = {k:table.get(v) if v in table.labels else np.atleast_2d([v]*len(table)).T for k,v in kwargs.items()}
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_,idx = np.unique(np.hstack(list(kwargs_.values())),return_index=True,axis=0)
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idx = np.sort(idx)
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kwargs_ = {k:np.atleast_1d(v[idx].squeeze()) for k,v in kwargs_.items()}
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return ConfigMaterial().material_add(**kwargs_)
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@property
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def is_complete(self) -> bool:
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"""
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Check for completeness.
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Only the general file layout is considered.
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This check does not consider whether parameters for
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a particular phase/homogenization model are missing.
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Returns
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-------
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complete : bool
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Whether the material.yaml definition is complete.
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"""
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ok = True
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for top_level in ['homogenization','phase','material']:
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ok &= top_level in self
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if top_level not in self: print(f'{top_level} entry missing')
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if ok:
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ok &= len(self['material']) > 0
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if len(self['material']) < 1: print('Incomplete material definition')
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if ok:
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homogenization = set()
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phase = set()
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for i,v in enumerate(self['material']):
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if 'homogenization' in v:
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homogenization.add(v['homogenization'])
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else:
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print(f'No homogenization specified in material {i}')
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ok = False
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if 'constituents' in v:
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for ii,vv in enumerate(v['constituents']):
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if 'O' not in vv:
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print('No orientation specified in constituent {ii} of material {i}')
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ok = False
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if 'phase' in vv:
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phase.add(vv['phase'])
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else:
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print(f'No phase specified in constituent {ii} of material {i}')
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ok = False
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for k,v in self['phase'].items():
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if 'lattice' not in v:
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print(f'No lattice specified in phase {k}')
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ok = False
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for k,v in self['homogenization'].items():
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if 'N_constituents' not in v:
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print(f'No. of constituents not specified in homogenization {k}')
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ok = False
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if phase - set(self['phase']):
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print(f'Phase(s) {phase-set(self["phase"])} missing')
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ok = False
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if homogenization - set(self['homogenization']):
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print(f'Homogenization(s) {homogenization-set(self["homogenization"])} missing')
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ok = False
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return ok
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@property
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def is_valid(self) -> bool:
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"""
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Check for valid content.
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Only the generic file content is considered.
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This check does not consider whether parameters for a
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particular phase/homogenization mode are out of bounds.
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Returns
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-------
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valid : bool
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Whether the material.yaml definition is valid.
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"""
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ok = True
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if 'phase' in self:
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for k,v in self['phase'].items():
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if 'lattice' in v:
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try:
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Orientation(lattice=v['lattice'])
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except KeyError:
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print(f"Invalid lattice '{v['lattice']}' in phase '{k}'")
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ok = False
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if 'material' in self:
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for i,m in enumerate(self['material']):
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if 'constituents' in m:
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v = 0.0
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for c in m['constituents']:
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v += float(c['v'])
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if 'O' in c:
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try:
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Rotation.from_quaternion(c['O'])
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except ValueError:
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print(f"Invalid orientation '{c['O']}' in material '{i}'")
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ok = False
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if not np.isclose(v,1.0):
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print(f"Total fraction v = {v} ≠ 1 in material '{i}'")
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ok = False
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return ok
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def material_rename_phase(self,
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mapping: Dict[str, str],
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ID: Sequence[int] = None,
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constituent: Sequence[int] = None) -> 'ConfigMaterial':
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"""
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Change phase name in material.
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Parameters
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----------
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mapping: dictionary
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Mapping from old name to new name
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ID: list of ints, optional
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Limit renaming to selected material IDs.
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constituent: list of ints, optional
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Limit renaming to selected constituents.
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Returns
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-------
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updated : damask.ConfigMaterial
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Updated material configuration.
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"""
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dup = self.copy()
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for i,m in enumerate(dup['material']):
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if ID is not None and i not in ID: continue
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for c in m['constituents']:
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if constituent is not None and c not in constituent: continue
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try:
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c['phase'] = mapping[c['phase']]
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except KeyError:
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continue
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return dup
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def material_rename_homogenization(self,
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mapping: Dict[str, str],
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ID: Sequence[int] = None) -> 'ConfigMaterial':
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"""
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Change homogenization name in material.
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Parameters
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----------
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mapping: dictionary
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Mapping from old name to new name
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ID: list of ints, optional
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Limit renaming to selected homogenization IDs.
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Returns
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-------
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updated : damask.ConfigMaterial
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Updated material configuration.
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"""
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dup = self.copy()
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for i,m in enumerate(dup['material']):
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if ID is not None and i not in ID: continue
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try:
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m['homogenization'] = mapping[m['homogenization']]
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except KeyError:
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continue
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return dup
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def material_add(self,
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**kwargs: Any) -> 'ConfigMaterial':
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"""
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Add material entries.
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Parameters
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----------
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**kwargs
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Key-value pairs.
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Returns
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-------
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updated : damask.ConfigMaterial
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Updated material configuration.
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Examples
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--------
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Create a dual-phase steel microstructure for micromechanical simulations:
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>>> import numpy as np
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>>> import damask
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>>> m = damask.ConfigMaterial()
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>>> m = m.material_add(phase = ['Ferrite','Martensite'],
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... O = damask.Rotation.from_random(2),
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... homogenization = 'SX')
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>>> m
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material:
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- constituents:
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- O: [0.577764, -0.146299, -0.617669, 0.513010]
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v: 1.0
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phase: Ferrite
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homogenization: SX
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- constituents:
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- O: [0.184176, 0.340305, 0.737247, 0.553840]
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v: 1.0
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phase: Martensite
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homogenization: SX
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homogenization: {}
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phase: {}
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Create a duplex stainless steel microstructure for forming simulations:
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>>> import numpy as np
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>>> import damask
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>>> m = damask.ConfigMaterial()
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>>> m = m.material_add(phase = np.array(['Austenite','Ferrite']).reshape(1,2),
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... O = damask.Rotation.from_random((2,2)),
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... v = np.array([0.2,0.8]).reshape(1,2),
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... homogenization = 'Taylor')
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>>> m
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material:
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- constituents:
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- phase: Austenite
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O: [0.659802978293224, 0.6953785848195171, 0.22426295326327111, -0.17554139512785227]
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v: 0.2
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- phase: Ferrite
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O: [0.49356745891301596, 0.2841806579193434, -0.7487679215072818, -0.339085707289975]
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v: 0.8
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homogenization: Taylor
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- constituents:
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- phase: Austenite
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O: [0.26542221365204055, 0.7268854930702071, 0.4474726435701472, -0.44828201137283735]
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v: 0.2
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- phase: Ferrite
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O: [0.6545817158479885, -0.08004812803625233, -0.6226561293931374, 0.4212059104577611]
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v: 0.8
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homogenization: Taylor
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homogenization: {}
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phase: {}
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"""
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N,n,shaped = 1,1,{}
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map_dim = {'O':-1,'V_e':-2}
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for k,v in kwargs.items():
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shaped[k] = np.array(v)
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s = shaped[k].shape[:map_dim.get(k,None)]
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N = max(N,s[0]) if len(s)>0 else N
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n = max(n,s[1]) if len(s)>1 else n
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mat: Sequence[dict] = [{'constituents':[{} for _ in range(n)]} for _ in range(N)]
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if 'v' not in kwargs:
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shaped['v'] = np.broadcast_to(1/n,(N,n))
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map_shape = {'O':(N,n,4),'V_e':(N,n,3,3)}
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for k,v in shaped.items():
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target = map_shape.get(k,(N,n))
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obj = np.broadcast_to(v.reshape(util.shapeshifter(v.shape, target, mode = 'right')), target)
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for i in range(N):
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if k in ['phase','O','v','V_e']:
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for j in range(n):
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mat[i]['constituents'][j][k] = obj[i,j].item() if isinstance(obj[i,j],np.generic) else obj[i,j]
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else:
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mat[i][k] = obj[i,0].item() if isinstance(obj[i,0],np.generic) else obj[i,0]
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dup = self.copy()
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dup['material'] = dup['material'] + mat if 'material' in dup else mat
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return dup
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