Merge branch 'master' into ci-update

CHANGELOG.rst

@@ -6,11 +6,27 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog`_,
 and this project adheres to `Semantic Versioning`_.
 
-`Unreleased`_
+`1.3.2`_ -  2020-07-11
+--------------------------
+Added
+'''''
+- VTK output for 2D triangular meshes.
+
+Changed
+'''''''
+- Updated reference to CMAME publication.
+
+`1.3.1`_ - 2020-07-09
 --------------------------
 Added
 '''''
 - VTK output for seed lists and polyhedral meshes.
+- Option to compute expected area of ellipse from area distribution.
+- Option to compute expected volume of ellipsoid from volume distribution.
+
+Fixed
+'''''
+- Error in verification module for 2D uniform random orientations.
 
 Changed
 '''''''
@@ -123,7 +139,9 @@ Added
 
 .. LINKS
 
-.. _`Unreleased`: https://github.com/kip-hart/MicroStructPy/compare/v1.3.0...HEAD
+.. _`Unreleased`: https://github.com/kip-hart/MicroStructPy/compare/v1.3.2...HEAD
+.. _`1.3.2`: https://github.com/kip-hart/MicroStructPy/compare/v1.3.1...v1.3.2
+.. _`1.3.1`: https://github.com/kip-hart/MicroStructPy/compare/v1.3.0...v1.3.1
 .. _`1.3.0`: https://github.com/kip-hart/MicroStructPy/compare/v1.2.2...v1.3.0
 .. _`1.2.2`: https://github.com/kip-hart/MicroStructPy/compare/v1.2.1...v1.2.2
 .. _`1.2.1`: https://github.com/kip-hart/MicroStructPy/compare/v1.2.0...v1.2.1

README.rst

@@ -140,8 +140,9 @@ in your bibliography:
 K. A. Hart and J. J. Rimoli, Generation of statistically representative
 microstructures with direct grain geomety control,
 *Computer Methods in Applied Mechanics and Engineering*,
-in press.
+370 (2020), pp. 113242.
 (`BibTeX <https://github.com/kip-hart/MicroStructPy/raw/master/docs/publications/cmame2020.bib>`_)
+(`DOI <https://doi.org/10.1016/j.cma.2020.113242>`_)
 
 .. end-publications
 
@@ -188,6 +189,6 @@ advised by Prof. Julian Rimoli.
     :target: https://github.com/kip-hart/MicroStructPy/blob/master/LICENSE.rst
     :alt: License
 
-.. |s-doi| image:: https://zenodo.org/badge/206468500.svg
-   :target: https://zenodo.org/badge/latestdoi/206468500
+.. |s-doi| image:: https://img.shields.io/badge/DOI-10.1016%2Fj.cma.2020.113242-blue
+   :target: https://doi.org/10.1016/j.cma.2020.113242
    :alt: DOI

docs/publications/cmame2020.bib

@@ -2,5 +2,12 @@ @article{Hart2020
     author = {Hart, Kenneth A and Rimoli, Julian J},
     title = {Generation of statistically representative microstructures with direct grain geomety control},
     journal = {Computer Methods in Applied Mechanics and Engineering},
-    year = {in press},
+    volume = {370},
+    pages = {113242},
+    year = {2020},
+    issn = {0045-7825},
+    doi = "https://doi.org/10.1016/j.cma.2020.113242",
+    url = "http://www.sciencedirect.com/science/article/pii/S0045782520304278",
+    keywords = "Microstructure, Polycrystal, Finite element modeling, Laguerre tessellation, Multi-sphere",
+    abstract = "Microstructural characteristics play a significant role in the determination of effective properties of materials. Consequently, most numerical tools aimed at predicting such properties require, as a starting point, the availability of geometric representations of such microstructures. In this paper, we introduce a method for generating statistically representative synthetic microstructures for materials involving multiple phases. Our method is based on traditional seed placement and tessellation approaches, with three critical improvements: (i) allowing for controlled seed overlap to better represent microstructural statistics, (ii) multi-sphere representation of 3D ellipsoids to account for arbitrarily elongated grains, and (iii) novel application of the axis aligned bounding box tree structure for accelerated seed placement. Our method recreates a diverse set of microstructural features, including the presence of spherical and non-spherical grain geometries, amorphous phases, and voids. After the method is presented, we proceed with a rigorous numerical analysis demonstrating its ability to reproduce key statistical features of target microstructures. The algorithms presented are freely available and open source through the package MicroStructPy."
 }

src/microstructpy/__init__.py

@@ -5,4 +5,4 @@
 import microstructpy.seeding
 import microstructpy.verification
 
-__version__ = '1.3.0'
+__version__ = '1.3.2'

src/microstructpy/geometry/ellipsoid.py

@@ -520,6 +520,14 @@ def volume_expectation(cls, **kwargs):
                 return 0.5 * np.pi * s_dist * s_dist * s_dist / 3
             return 0.5 * np.pi * s_dist.moment(3) / 3
 
+        if 'volume' in kwargs:
+            v_dist = kwargs['volume']
+            try:
+                v_exp = v_dist.moment(1)
+            except AttributeError:
+                v_exp = v_dist
+            return v_exp
+
         # check for a, b, and c distribution
         try:
             exp_vol = 4 * np.pi / 3

src/microstructpy/geometry/m_ellipse.py

@@ -252,6 +252,14 @@ def area_expectation(cls, **kwargs):
                 return 0.25 * np.pi * s_dist * s_dist
             return 0.25 * np.pi * s_dist.moment(2)
 
+        if 'area' in kwargs:
+            a_dist = kwargs['area']
+            try:
+                a_exp = a_dist.moment(1)
+            except AttributeError:
+                a_exp = a_dist
+            return a_exp
+
         if ('a' in kwargs) and ('b' in kwargs):
             exp = np.pi
             for kw in ('a', 'b'):

src/microstructpy/meshing/trimesh.py

@@ -590,28 +590,35 @@ def write(self, filename, format='txt', seeds=None, polymesh=None):
                     file.write(edge)
 
         elif fmt == 'vtk':
-            assert len(self.points[0]) == 3
+            n_kp = len(self.elements[0])
+            mesh_type = {3: 'Triangular', 4: 'Tetrahedral'}[n_kp]
             pt_fmt = '{: f} {: f} {: f}\n'
             # write heading
             vtk = '# vtk DataFile Version 2.0\n'
-            vtk += 'Tetrahedral mesh\n'
+            vtk += '{} mesh\n'.format(mesh_type)
             vtk += 'ASCII\n'
             vtk += 'DATASET UNSTRUCTURED_GRID\n'
 
             # Write points
             vtk += 'POINTS ' + str(len(self.points)) + ' float\n'
-            vtk += ''.join([pt_fmt.format(x, y, z) for x, y, z in self.points])
+            if len(self.points[0]) == 2:
+                vtk += ''.join([pt_fmt.format(x, y, 0) for x, y in
+                                self.points])
+            else:
+                vtk += ''.join([pt_fmt.format(x, y, z) for x, y, z in
+                                self.points])
 
             # write elements
             n_elem = len(self.elements)
-            cell_sz = 5 * n_elem
+            cell_fmt = str(n_kp) + n_kp * ' {}' + '\n'
+            cell_sz = (1 + n_kp) * n_elem
             vtk += '\nCELLS ' + str(n_elem) + ' ' + str(cell_sz) + '\n'
-            vtk += ''.join(['4 ' + ' '.join([str(k) for k in el]) + '\n' for
-                            el in self.elements])
+            vtk += ''.join([cell_fmt.format(*el) for el in self.elements])
 
             # write cell type
             vtk += '\nCELL_TYPES ' + str(n_elem) + '\n'
-            vtk += ''.join(n_elem * ['10\n'])
+            cell_type =  {3: '5', 4: '10'}[n_kp]
+            vtk += ''.join(n_elem * [cell_type + '\n'])
 
             # write element attributes
             try:

src/microstructpy/verification.py

@@ -893,6 +893,11 @@ def error_stats(fit_seeds, seeds, phases, poly_mesh=None, verif_mask=None):
         i_phase = init_phases[i]
         o_phase = outp_phases[i]
         phase = phases[i]
+        for kw in phase:
+            if kw in ('angle', 'angle_deg') and phase[kw] == 'random':
+                phase[kw] = scipy.stats.uniform(loc=0, scale=360)
+            if kw == 'angle_rad':
+                phase[kw] = scipy.stats.uniform(loc=0, scale=2 * np.pi)
 
         err_io = {kw: _kw_errs(i_phase[kw], o_phase[kw]) for kw in i_phase}
         err_po = {kw: _kw_stats(phase[kw], o_phase[kw]) for kw in o_phase}