From 07d79ef4ba3101d5e1c638d3a9bd6facad68aeec Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 17 Mar 2021 11:25:21 +0100 Subject: [PATCH 1/4] unifying style --- python/damask/_colormap.py | 14 ++++++++------ src/grid/spectral_utilities.f90 | 8 ++++---- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py index 7e8860dae..d14503f5c 100644 --- a/python/damask/_colormap.py +++ b/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 + http://dx.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 """ diff --git a/src/grid/spectral_utilities.f90 b/src/grid/spectral_utilities.f90 index e8bae223a..97801cfb3 100644 --- a/src/grid/spectral_utilities.f90 +++ b/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' !-------------------------------------------------------------------------------------------------- From fc172921fb79b3b5fe40b1927e262baebb5532d5 Mon Sep 17 00:00:00 2001 From: Sharan Roongta Date: Thu, 18 Mar 2021 15:36:40 +0100 Subject: [PATCH 2/4] unified citation style continued --- python/damask/_grid.py | 11 +++-------- python/damask/_orientation.py | 6 ++---- python/damask/_rotation.py | 8 +++----- src/DAMASK_interface.f90 | 2 +- src/grid/DAMASK_grid.f90 | 2 +- src/grid/grid_damage_spectral.f90 | 2 +- src/grid/grid_mech_spectral_basic.f90 | 4 ++-- src/grid/grid_mech_spectral_polarisation.f90 | 2 +- src/grid/grid_thermal_spectral.f90 | 2 +- src/homogenization_mechanical_RGC.f90 | 7 +++---- src/phase_mechanical_plastic_dislotungsten.f90 | 2 +- src/phase_mechanical_plastic_dislotwin.f90 | 6 +++--- src/phase_mechanical_plastic_isotropic.f90 | 2 +- src/phase_mechanical_plastic_nonlocal.f90 | 4 ++-- src/results.f90 | 2 +- src/rotations.f90 | 2 +- 16 files changed, 27 insertions(+), 37 deletions(-) diff --git a/python/damask/_grid.py b/python/damask/_grid.py index a58f2ca2c..8ce98b09a 100644 --- a/python/damask/_grid.py +++ b/python/damask/_grid.py @@ -482,18 +482,13 @@ 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 """ diff --git a/python/damask/_orientation.py b/python/damask/_orientation.py index a14af98af..f05f47544 100644 --- a/python/damask/_orientation.py +++ b/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 """ diff --git a/python/damask/_rotation.py b/python/damask/_rotation.py index 34a5f81b7..40078e4d5 100644 --- a/python/damask/_rotation.py +++ b/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 """ diff --git a/src/DAMASK_interface.f90 b/src/DAMASK_interface.f90 index ab64dcf01..b7cb1d80f 100644 --- a/src/DAMASK_interface.f90 +++ b/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 diff --git a/src/grid/DAMASK_grid.f90 b/src/grid/DAMASK_grid.f90 index 0aa462e7e..0cefc79a6 100644 --- a/src/grid/DAMASK_grid.f90 +++ b/src/grid/DAMASK_grid.f90 @@ -118,7 +118,7 @@ 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' diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90 index 8d3f913fa..6f99365f7 100644 --- a/src/grid/grid_damage_spectral.f90 +++ b/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' !------------------------------------------------------------------------------------------------- diff --git a/src/grid/grid_mech_spectral_basic.f90 b/src/grid/grid_mech_spectral_basic.f90 index faf58c85e..e7690eb55 100644 --- a/src/grid/grid_mech_spectral_basic.f90 +++ b/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' !------------------------------------------------------------------------------------------------- diff --git a/src/grid/grid_mech_spectral_polarisation.f90 b/src/grid/grid_mech_spectral_polarisation.f90 index 31f69b4c5..478df7fdf 100644 --- a/src/grid/grid_mech_spectral_polarisation.f90 +++ b/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' !------------------------------------------------------------------------------------------------- diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90 index 5ac043a67..dd431ad9b 100644 --- a/src/grid/grid_thermal_spectral.f90 +++ b/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' !------------------------------------------------------------------------------------------------- diff --git a/src/homogenization_mechanical_RGC.f90 b/src/homogenization_mechanical_RGC.f90 index a68e9b772..581aa1c8e 100644 --- a/src/homogenization_mechanical_RGC.f90 +++ b/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') diff --git a/src/phase_mechanical_plastic_dislotungsten.f90 b/src/phase_mechanical_plastic_dislotungsten.f90 index 1fda51a58..95234a2e2 100644 --- a/src/phase_mechanical_plastic_dislotungsten.f90 +++ b/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' diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90 index 5500ae731..f9bf0a652 100644 --- a/src/phase_mechanical_plastic_dislotwin.f90 +++ b/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' diff --git a/src/phase_mechanical_plastic_isotropic.f90 b/src/phase_mechanical_plastic_isotropic.f90 index d02436fba..a339d85a6 100644 --- a/src/phase_mechanical_plastic_isotropic.f90 +++ b/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') diff --git a/src/phase_mechanical_plastic_nonlocal.f90 b/src/phase_mechanical_plastic_nonlocal.f90 index d0007075b..482c31abd 100644 --- a/src/phase_mechanical_plastic_nonlocal.f90 +++ b/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' diff --git a/src/results.f90 b/src/results.f90 index c9c51b9a2..45629b2ab 100644 --- a/src/results.f90 +++ b/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 diff --git a/src/rotations.f90 b/src/rotations.f90 index 57dd16b53..171db2466 100644 --- a/src/rotations.f90 +++ b/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 From 7012099d0c329cc622e12ced57aefd71f089af1d Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 20 Mar 2021 14:34:14 +0100 Subject: [PATCH 3/4] substituted broken link --- python/damask/_colormap.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py index d14503f5c..2b8782134 100644 --- a/python/damask/_colormap.py +++ b/python/damask/_colormap.py @@ -526,7 +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([ @@ -546,7 +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) From 0e571352392cbd0ad3fa5eaf3e97331b01073e57 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Thu, 25 Mar 2021 14:33:08 -0400 Subject: [PATCH 4/4] [skip ci] dx.doi.org --> doi.org --- python/damask/_colormap.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py index 2b8782134..639a5a04c 100644 --- a/python/damask/_colormap.py +++ b/python/damask/_colormap.py @@ -28,7 +28,7 @@ class Colormap(mpl.colors.ListedColormap): References ---------- K. Moreland, Proceedings of the 5th International Symposium on Advances in Visual Computing, 2009 - http://dx.doi.org/10.1007/978-3-642-10520-3_9 + 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