Merge branch 'development' into output-rename

python/damask/_colormap.py

@@ -27,12 +27,14 @@ class Colormap(mpl.colors.ListedColormap):
 
     References
     ----------
-    [1] DAMASK colormap theory
-      https://www.kennethmoreland.com/color-maps/ColorMapsExpanded.pdf
-    [2] DAMASK colormaps first use
-      https://doi.org/10.1016/j.ijplas.2012.09.012
-    [3] Matplotlib colormaps overview
-      https://matplotlib.org/tutorials/colors/colormaps.html
+    K. Moreland, Proceedings of the 5th International Symposium on Advances in Visual Computing, 2009
+    https://doi.org/10.1007/978-3-642-10520-3_9
+
+    P. Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013
+    https://doi.org/10.1016/j.ijplas.2012.09.012
+
+    Matplotlib colormaps overview
+    https://matplotlib.org/tutorials/colors/colormaps.html
 
     """
 
@@ -524,7 +526,7 @@ class Colormap(mpl.colors.ListedColormap):
 
         References
         ----------
-        http://www.ryanjuckett.com/programming/rgb-color-space-conversion
+        https://www.easyrgb.com/en/math.php
 
         """
         rgb_lin = np.dot(np.array([
@@ -544,7 +546,7 @@ class Colormap(mpl.colors.ListedColormap):
 
         References
         ----------
-        http://www.ryanjuckett.com/programming/rgb-color-space-conversion
+        https://www.easyrgb.com/en/math.php
 
         """
         rgb_lin = np.where(rgb>0.04045,((rgb+0.0555)/1.0555)**2.4,rgb/12.92)

python/damask/_grid.py

@@ -509,18 +509,13 @@ class Grid:
 
         References
         ----------
-        Sébastien B G Blanquer, Maike Werner, Markus Hannula, Shahriar Sharifi,
-        Guillaume P R Lajoinie, David Eglin, Jari Hyttinen, André A Poot, and Dirk W Grijpma
-        Surface curvature in triply-periodic minimal surface architectures as
-        a distinct design parameter in preparing advanced tissue engineering scaffolds
+        S.B.G. Blanquer et al., Biofabrication 9(2):025001, 2017
         https://doi.org/10.1088/1758-5090/aa6553
 
-        Meinhard Wohlgemuth, Nataliya Yufa, James Hoffman, and Edwin L. Thomas
-        Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
+        M. Wohlgemuth et al., Macromolecules 34(17):6083-6089, 2001
         https://doi.org/10.1021/ma0019499
 
-        Meng-Ting Hsieh, Lorenzo Valdevit
-        Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
+        M.-T. Hsieh and L. Valdevit, Software Impacts 6:100026, 2020
         https://doi.org/10.1016/j.simpa.2020.100026
 
         """

python/damask/_orientation.py

@@ -742,8 +742,7 @@ class Orientation(Rotation):
 
         References
         ----------
-        C.T. Young and J.L. Lytton, J. Appl. Phys. 43:1408–1417, 1972
-        "Computer Generation and Identification of Kikuchi Projections"
+        C.T. Young and J.L. Lytton, Journal of Applied Physics 43:1408–1417, 1972
         https://doi.org/10.1063/1.1661333
 
         """
@@ -1070,8 +1069,7 @@ class Orientation(Rotation):
 
         References
         ----------
-        J.C. Glez and J. Driver, J. Appl. Cryst. 34:280-288, 2001
-        "Orientation distribution analysis in deformed grains"
+        J.C. Glez and J. Driver, Journal of Applied Crystallography 34:280-288, 2001
         https://doi.org/10.1107/S0021889801003077
 
         """

python/damask/_rotation.py

@@ -357,10 +357,8 @@ class Rotation:
 
         References
         ----------
-        Quaternion averaging
-        F. Landis Markley, Yang Cheng, John L. Crassidis, Yaakov Oshman
-        Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
-        10.2514/1.28949
+        F. Landis Markley et al., Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
+        https://doi.org/10.2514/1.28949
 
         """
         def _M(quat):
@@ -859,7 +857,7 @@ class Rotation:
 
         References
         ----------
-        P. Eisenlohr, F. Roters, Computational Materials Science 42(4), 670-678, 2008
+        P. Eisenlohr and F. Roters, Computational Materials Science 42(4):670-678, 2008
         https://doi.org/10.1016/j.commatsci.2007.09.015
 
         """

src/DAMASK_interface.f90

@@ -93,7 +93,7 @@ subroutine DAMASK_interface_init
 #endif
   print*, achar(27)//'[0m'
 
-  print*, 'Roters et al., Computational Materials Science 158:420–478, 2019'
+  print*, 'F. Roters et al., Computational Materials Science 158:420–478, 2019'
   print*, 'https://doi.org/10.1016/j.commatsci.2018.04.030'
 
   print'(/,a)', ' Version: '//DAMASKVERSION

src/grid/DAMASK_grid.f90

@@ -117,7 +117,7 @@ program DAMASK_grid
   call CPFEM_initAll
   print'(/,a)',   ' <<<+-  DAMASK_grid init  -+>>>'; flush(IO_STDOUT)
 
-  print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
+  print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
   print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
 
 

src/grid/grid_damage_spectral.f90

@@ -75,7 +75,7 @@ subroutine grid_damage_spectral_init
 
   print'(/,a)', ' <<<+-  grid_spectral_damage init  -+>>>'
 
-  print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
+  print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
   print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
 
 !-------------------------------------------------------------------------------------------------

src/grid/grid_mech_spectral_basic.f90

@@ -105,10 +105,10 @@ subroutine grid_mechanical_spectral_basic_init
 
   print'(/,a)', ' <<<+-  grid_mechanical_spectral_basic init  -+>>>'; flush(IO_STDOUT)
 
-  print*, 'Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
+  print*, 'P. Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
   print*, 'https://doi.org/10.1016/j.ijplas.2012.09.012'//IO_EOL
 
-  print*, 'Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
+  print*, 'P. Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
   print*, 'https://doi.org/10.1016/j.ijplas.2014.02.006'
 
 !-------------------------------------------------------------------------------------------------

src/grid/grid_mech_spectral_polarisation.f90

@@ -118,7 +118,7 @@ subroutine grid_mechanical_spectral_polarisation_init
 
   print'(/,a)', ' <<<+-  grid_mechanical_spectral_polarization init  -+>>>'; flush(IO_STDOUT)
 
-  print*, 'Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
+  print*, 'P. Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
   print*, 'https://doi.org/10.1016/j.ijplas.2014.02.006'
 
 !-------------------------------------------------------------------------------------------------

src/grid/grid_thermal_spectral.f90

@@ -75,7 +75,7 @@ subroutine grid_thermal_spectral_init(T_0)
 
   print'(/,a)', ' <<<+-  grid_thermal_spectral init  -+>>>'
 
-  print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
+  print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
   print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
 
 !-------------------------------------------------------------------------------------------------

src/grid/spectral_utilities.f90

@@ -176,16 +176,16 @@ subroutine spectral_utilities_init
 
   print'(/,a)', ' <<<+-  spectral_utilities init  -+>>>'
 
-  print*, 'Diehl, Diploma Thesis TU München, 2010'
+  print*, 'M. Diehl, Diploma Thesis TU München, 2010'
   print*, 'https://doi.org/10.13140/2.1.3234.3840'//IO_EOL
 
-  print*, 'Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
+  print*, 'P. Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
   print*, 'https://doi.org/10.1016/j.ijplas.2012.09.012'//IO_EOL
 
-  print*, 'Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
+  print*, 'P. Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
   print*, 'https://doi.org/10.1016/j.ijplas.2014.02.006'//IO_EOL
 
-  print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
+  print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
   print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
 
 !--------------------------------------------------------------------------------------------------

src/homogenization_mechanical_RGC.f90

@@ -91,12 +91,11 @@ module subroutine mechanical_RGC_init(num_homogMech)
 
   print'(a,i2)', ' # instances: ',count(homogenization_type == HOMOGENIZATION_RGC_ID); flush(IO_STDOUT)
 
-  print*, 'Tjahjanto et al., International Journal of Material Forming 2(1):939–942, 2009'
+  print*, 'D.D. Tjahjanto et al., International Journal of Material Forming 2(1):939–942, 2009'
   print*, 'https://doi.org/10.1007/s12289-009-0619-1'//IO_EOL
 
-  print*, 'Tjahjanto et al., Modelling and Simulation in Materials Science and Engineering 18:015006, 2010'
-  print*,   'https://doi.org/10.1088/0965-0393/18/1/015006'//IO_EOL
-
+  print*, 'D.D. Tjahjanto et al., Modelling and Simulation in Materials Science and Engineering 18:015006, 2010'
+  print*, 'https://doi.org/10.1088/0965-0393/18/1/015006'//IO_EOL
 
 
   material_homogenization => config_material%get('homogenization')

src/phase_mechanical_plastic_dislotungsten.f90

@@ -103,7 +103,7 @@ module function plastic_dislotungsten_init() result(myPlasticity)
   print'(/,a)', ' <<<+-  phase:mechanical:plastic:dislotungsten init  -+>>>'
   print'(a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
 
-  print*, 'Cereceda et al., International Journal of Plasticity 78:242–256, 2016'
+  print*, 'D. Cereceda et al., International Journal of Plasticity 78:242–256, 2016'
   print*, 'https://dx.doi.org/10.1016/j.ijplas.2015.09.002'
 
 

src/phase_mechanical_plastic_dislotwin.f90

@@ -150,13 +150,13 @@ module function plastic_dislotwin_init() result(myPlasticity)
   print'(/,a)', ' <<<+-  phase:mechanical:plastic:dislotwin init  -+>>>'
   print'(a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
 
-  print*, 'Ma and Roters, Acta Materialia 52(12):3603–3612, 2004'
+  print*, 'A. Ma and F. Roters, Acta Materialia 52(12):3603–3612, 2004'
   print*, 'https://doi.org/10.1016/j.actamat.2004.04.012'//IO_EOL
 
-  print*, 'Roters et al., Computational Materials Science 39:91–95, 2007'
+  print*, 'F. Roters et al., Computational Materials Science 39:91–95, 2007'
   print*, 'https://doi.org/10.1016/j.commatsci.2006.04.014'//IO_EOL
 
-  print*, 'Wong et al., Acta Materialia 118:140–151, 2016'
+  print*, 'S.L. Wong et al., Acta Materialia 118:140–151, 2016'
   print*, 'https://doi.org/10.1016/j.actamat.2016.07.032'
 
 

src/phase_mechanical_plastic_isotropic.f90

@@ -71,7 +71,7 @@ module function plastic_isotropic_init() result(myPlasticity)
   print'(/,a)', ' <<<+-  phase:mechanical:plastic:isotropic init  -+>>>'
   print'(a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
 
-  print*, 'Maiti and Eisenlohr, Scripta Materialia 145:37–40, 2018'
+  print*, 'T. Maiti and P. Eisenlohr, Scripta Materialia 145:37–40, 2018'
   print*, 'https://doi.org/10.1016/j.scriptamat.2017.09.047'
 
   phases => config_material%get('phase')

src/phase_mechanical_plastic_nonlocal.f90

@@ -203,10 +203,10 @@ module function plastic_nonlocal_init() result(myPlasticity)
   print'(/,a)', ' <<<+-  phase:mechanical:plastic:nonlocal init  -+>>>'
   print'(a,i0)', ' # phases: ',Ninstances; flush(IO_STDOUT)
 
-  print*, 'Reuber et al., Acta Materialia 71:333–348, 2014'
+  print*, 'C. Reuber et al., Acta Materialia 71:333–348, 2014'
   print*, 'https://doi.org/10.1016/j.actamat.2014.03.012'//IO_EOL
 
-  print*, 'Kords, Dissertation RWTH Aachen, 2014'
+  print*, 'C. Kords, Dissertation RWTH Aachen, 2014'
   print*, 'http://publications.rwth-aachen.de/record/229993'
 
 

src/results.f90

@@ -61,7 +61,7 @@ subroutine results_init(restart)
 
   print'(/,a)', ' <<<+-  results init  -+>>>'; flush(IO_STDOUT)
 
-  print*, 'Diehl et al., Integrating Materials and Manufacturing Innovation 6(1):83–91, 2017'
+  print*, 'M. Diehl et al., Integrating Materials and Manufacturing Innovation 6(1):83–91, 2017'
   print*, 'https://doi.org/10.1007/s40192-017-0084-5'//IO_EOL
 
   if(.not. restart) then

src/rotations.f90

@@ -105,7 +105,7 @@ subroutine rotations_init
 
   print'(/,a)', ' <<<+-  rotations init  -+>>>'; flush(IO_STDOUT)
 
-  print*, 'Rowenhorst et al., Modelling and Simulation in Materials Science and Engineering 23:083501, 2015'
+  print*, 'D. Rowenhorst et al., Modelling and Simulation in Materials Science and Engineering 23:083501, 2015'
   print*, 'https://doi.org/10.1088/0965-0393/23/8/083501'
 
   call selfTest