Merge pull request #256 from pyiron/damask_imports

[Damask] update import names

.ci_support/environment-notebooks-damask.yml

@@ -5,16 +5,15 @@ dependencies:
   - coveralls
   - coverage
   - codacy-coverage
-  - damask-mesh =3.0.0a8
-  - damask-grid =3.0.0a8
-  - damask =3.0.0a8
-  - mshr =2019.1.0=*_9
-  - k3d =2.16.0
+  - damask-mesh =3.0.0b
+  - damask-grid =3.0.0b
+  - damask =3.0.0b
+  - k3d
   - matplotlib =3.8.0
   - numpy =1.26.3
   - pyiron =0.5.0
-  - pyiron-data =0.0.26
-  - python-damask =3.0.0a8
+  - pyiron-data
+  - python-damask =3.0.0b
   - pyvista =0.42.3
   - scipy =1.11.4
   - seaborn =0.13.1

.ci_support/environment-notebooks-fenics.yml

@@ -7,8 +7,8 @@ dependencies:
   - codacy-coverage
   - fenics =2019.1.0
   - fenics =2019.1.0=*_42
-  - mshr =2019.1.0=*_9
-  - k3d =2.16.0
+  - mshr
+  - k3d
   - matplotlib =3.8.0
   - numpy =1.26.3
   - pyiron =0.5.0

.ci_support/environment-notebooks.yml

@@ -5,9 +5,9 @@ dependencies:
   - coveralls
   - coverage
   - codacy-coverage
-  - damask-mesh =3.0.0a8
-  - damask-grid =3.0.0a8
-  - damask =3.0.0a8
+  - damask-mesh =3.0.0b
+  - damask-grid =3.0.0b
+  - damask =3.0.0b
   - fenics =2019.1.0
   - fenics =2019.1.0=*_42
   - mshr =2019.1.0=*_9
@@ -16,7 +16,7 @@ dependencies:
   - numpy =1.26.3
   - pyiron =0.5.0
   - pyiron-data =0.0.26
-  - python-damask =3.0.0a8
+  - python-damask =3.0.0b
   - pyvista =0.42.3
   - scipy =1.11.4
   - seaborn =0.13.1

pyiron_continuum/damask/factory.py

@@ -8,7 +8,7 @@
         'DAMASK functionality requires the `damask` module (and its dependencies) specified as extra'
         'requirements. Please install it and try again.'
 ) as damask_alarm:
-    from damask import Grid, Config, ConfigMaterial, seeds
+    from damask import GeomGrid, YAML, ConfigMaterial, seeds
 import numpy as np
 
 __author__ = "Muhammad Hassani"
@@ -49,22 +49,22 @@ def write(file_path):
 
 class GridFactory:
     def __init__(self):
-        """A factory for damask._grid.Grid class."""
+        """A factory for damask._grid.GeomGrid class."""
         self._origin = None
 
     @staticmethod
     def read(file_path):
-        return Grid.load(fname=file_path)
+        return GeomGrid.load(fname=file_path)
 
     @property
     def origin(self):
         """
-        Returns damask._grid.Grid, it can be used to call damask original methods.
+        Returns damask._grid.GeomGrid, it can be used to call damask original methods.
         For example:
         origin.from_Voronoi_tessellation(...)
         """
         if self._origin is None:
-            return Grid(material=np.ones((1, 1, 1)), size=[1., 1., 1.])
+            return GeomGrid(material=np.ones((1, 1, 1)), size=[1., 1., 1.])
         else:
             return self._origin
 
@@ -79,12 +79,12 @@ def via_voronoi_tessellation(spatial_discretization, num_grains, box_size):
         if isinstance(box_size, int) or isinstance(box_size, float):
             box_size = np.array([box_size, box_size, box_size])
         seed = seeds.from_random(box_size, num_grains)
-        return Grid.from_Voronoi_tessellation(spatial_discretization, box_size, seed)
+        return GeomGrid.from_Voronoi_tessellation(spatial_discretization, box_size, seed)
 
 
 class DamaskLoading(dict):
     def __init__(self, solver, load_steps):
-        """A factory for damask Loading class, which is a damask._config.Config object."""
+        """A factory for damask Loading class, which is a damask._config.YAML object."""
         super(DamaskLoading, self).__init__(self)
 
     def __new__(cls, solver, load_steps):
@@ -102,7 +102,7 @@ def __new__(cls, solver, load_steps):
                          discretization=load_steps['discretization'],
                          additional_parameters_dict=load_steps["additional"])
             ]
-        return Config(solver=loading_dict["solver"], loadstep=loading_dict["loadstep"])
+        return YAML(solver=loading_dict["solver"], loadstep=loading_dict["loadstep"])
 
 
 class LoadStep(dict):

pyiron_continuum/damask/regrid.py

@@ -11,7 +11,7 @@ def regrid_Geom(work_dir, geom_name, load_name, seed_scale=1.0, increment='last'
     Regrid the geometry
     It requires the previous geom.vti and result.hdf5
     '''
-    geom_0 = damask.Grid.load(f'{geom_name}.vti')
+    geom_0 = damask.GeomGrid.load(f'{geom_name}.vti')
     cells_0 = geom_0.cells
     size_0 = geom_0.size
 
@@ -26,11 +26,11 @@ def regrid_Geom(work_dir, geom_name, load_name, seed_scale=1.0, increment='last'
     d5Out = damask.Result(f'{work_dir}/{geom_name}_{load_name}_material.hdf5')
 
     if increment == 'last':
-        inc = int(d5Out.increments[-1][10::])  # take the increment number
+        inc = int(d5Out.increments[-1])  # take the increment number
         d5Out = d5Out.view(increments=inc)
         increment_title = d5Out.increments[-1]
     elif increment in d5Out.increments:
-        inc = int(increment[10::])  # take the increment number
+        inc = int(increment)  # take the increment number
         d5Out = d5Out.view(increments=inc)
         increment_title = increment
     else:
@@ -75,9 +75,9 @@ def write_RegriddedGeom(work_dir, geom_name, increment_title, map_0to_rg, cells_
     Save the regridded geometry to a new vti file
     '''
     os.chdir(f'{work_dir}')
-    grid_0 = damask.Grid.load(geom_name + '.vti')
+    grid_0 = damask.GeomGrid.load(geom_name + '.vti')
     material_rg = grid_0.material.flatten('F')[map_0to_rg].reshape(cells_rg, order='F')
-    grid = damask.Grid(material_rg, size_rg, grid_0.origin, comments=grid_0.comments \
+    grid = damask.GeomGrid(material_rg, size_rg, grid_0.origin, comments=grid_0.comments \
                        ).save(f'{geom_name}_regridded_{increment_title}.vti')
     print(f'save regrid geometry to {geom_name}_regridded_{increment_title}.vti')
     regrid_geom_name = f'{geom_name}_regridded_{increment_title}'

pyiron_continuum/damask/rolling.py

@@ -1,5 +1,4 @@
 from ast import arg
-import imp
 import os
 from random import vonmisesvariate
 import numpy as np
@@ -14,8 +13,7 @@
 
 from damaskjob import DAMASK
 import regrid as rgg
-from damask import Result
-from damask import Config
+from damask import Result, YAML
 from factory import DamaskLoading
 
 
@@ -33,7 +31,7 @@ def __init__(self, project, job_name):
     def loading_discretization(self, rolltimes, filename):
         time = rolltimes * self._height_reduction / (self._rolling_speed * self._number_passes)
 
-        self.load_case = Config(solver={'mechanical': 'spectral_basic'}, loadstep=[])
+        self.load_case = YAML(solver={'mechanical': 'spectral_basic'}, loadstep=[])
         dotF = [['x', 0, 0],
                 [0, 0, 0],
                 [0, 0, -1.0 * self._rolling_speed]]
@@ -72,7 +70,7 @@ def executeRolling(self, reduction_height, reduction_speed, reduction_outputs, r
             self._write_material()
             self._write_geometry()
 
-            self.load_case = Config(solver={'mechanical': 'spectral_basic'}, loadstep=[])
+            self.load_case = YAML(solver={'mechanical': 'spectral_basic'}, loadstep=[])
             reduction_time = reduction_height / reduction_speed
             dotF = [['x', 0, 0],
                     [0, 0, 0],