Merge remote-tracking branch 'origin/T_ref300' into dynamic-C

This commit is contained in:
Sharan Roongta 2021-11-25 11:18:25 +01:00
commit 8b06d97e84
10 changed files with 78 additions and 56 deletions

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@ -1 +1 @@
v3.0.0-alpha5-155-gbf76d9f3a
v3.0.0-alpha5-164-gdc993bc6f

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@ -2,6 +2,9 @@ import os
import json
import functools
import colorsys
from pathlib import Path
from typing import Sequence, Union, TextIO
import numpy as np
import matplotlib as mpl
@ -39,20 +42,20 @@ class Colormap(mpl.colors.ListedColormap):
"""
def __add__(self,other):
def __add__(self, other: "Colormap") -> "Colormap":
"""Concatenate."""
return Colormap(np.vstack((self.colors,other.colors)),
f'{self.name}+{other.name}')
def __iadd__(self,other):
def __iadd__(self, other: "Colormap") -> "Colormap":
"""Concatenate (in-place)."""
return self.__add__(other)
def __invert__(self):
def __invert__(self) -> "Colormap":
"""Reverse."""
return self.reversed()
def __repr__(self):
def __repr__(self) -> str:
"""Show as matplotlib figure."""
fig = plt.figure(self.name,figsize=(5,.5))
ax1 = fig.add_axes([0, 0, 1, 1])
@ -64,7 +67,11 @@ class Colormap(mpl.colors.ListedColormap):
@staticmethod
def from_range(low,high,name='DAMASK colormap',N=256,model='rgb'):
def from_range(low: Sequence[float],
high: Sequence[float],
name: str = 'DAMASK colormap',
N: int = 256,
model: str = 'rgb') -> "Colormap":
"""
Create a perceptually uniform colormap between given (inclusive) bounds.
@ -145,7 +152,7 @@ class Colormap(mpl.colors.ListedColormap):
@staticmethod
def from_predefined(name,N=256):
def from_predefined(name: str, N: int = 256) -> "Colormap":
"""
Select from a set of predefined colormaps.
@ -185,7 +192,10 @@ class Colormap(mpl.colors.ListedColormap):
return Colormap.from_range(definition['low'],definition['high'],name,N)
def shade(self,field,bounds=None,gap=None):
def shade(self,
field: np.ndarray,
bounds: Sequence[float] = None,
gap: float = None) -> Image:
"""
Generate PIL image of 2D field using colormap.
@ -226,7 +236,7 @@ class Colormap(mpl.colors.ListedColormap):
mode='RGBA')
def reversed(self,name=None):
def reversed(self, name: str = None) -> "Colormap":
"""
Reverse.
@ -251,7 +261,7 @@ class Colormap(mpl.colors.ListedColormap):
return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
def _get_file_handle(self,fname,extension):
def _get_file_handle(self, fname: Union[TextIO, str, Path, None], suffix: str) -> TextIO:
"""
Provide file handle.
@ -259,8 +269,7 @@ class Colormap(mpl.colors.ListedColormap):
----------
fname : file, str, pathlib.Path, or None
Filename or filehandle, will be name of the colormap+extension if None.
extension: str
suffix: str
Extension of the filename.
Returns
@ -270,17 +279,14 @@ class Colormap(mpl.colors.ListedColormap):
"""
if fname is None:
fhandle = open(self.name.replace(' ','_')+'.'+extension,'w',newline='\n')
return open(self.name.replace(' ','_')+suffix, 'w', newline='\n')
elif isinstance(fname, (str, Path)):
return open(fname, 'w', newline='\n')
else:
try:
fhandle = open(fname,'w',newline='\n')
except TypeError:
fhandle = fname
return fhandle
return fname
def save_paraview(self,fname=None):
def save_paraview(self, fname: Union[TextIO, str, Path] = None):
"""
Save as JSON file for use in Paraview.
@ -303,10 +309,10 @@ class Colormap(mpl.colors.ListedColormap):
'RGBPoints':colors
}]
json.dump(out,self._get_file_handle(fname,'json'),indent=4)
json.dump(out,self._get_file_handle(fname,'.json'),indent=4)
def save_ASCII(self,fname=None):
def save_ASCII(self, fname: Union[TextIO, str, Path] = None):
"""
Save as ASCII file.
@ -319,10 +325,10 @@ class Colormap(mpl.colors.ListedColormap):
"""
labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
t = Table(self.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
t.save(self._get_file_handle(fname,'txt'))
t.save(self._get_file_handle(fname,'.txt'))
def save_GOM(self,fname=None):
def save_GOM(self, fname: Union[TextIO, str, Path] = None):
"""
Save as ASCII file for use in GOM Aramis.
@ -340,10 +346,10 @@ class Colormap(mpl.colors.ListedColormap):
+ ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(int))]) \
+ '\n'
self._get_file_handle(fname,'legend').write(GOM_str)
self._get_file_handle(fname,'.legend').write(GOM_str)
def save_gmsh(self,fname=None):
def save_gmsh(self, fname: Union[TextIO, str, Path] = None):
"""
Save as ASCII file for use in gmsh.
@ -358,11 +364,13 @@ class Colormap(mpl.colors.ListedColormap):
gmsh_str = 'View.ColorTable = {\n' \
+'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
+'\n}\n'
self._get_file_handle(fname,'msh').write(gmsh_str)
self._get_file_handle(fname,'.msh').write(gmsh_str)
@staticmethod
def _interpolate_msh(frac,low,high):
def _interpolate_msh(frac,
low: np.ndarray,
high: np.ndarray) -> np.ndarray:
"""
Interpolate in Msh color space.
@ -439,31 +447,31 @@ class Colormap(mpl.colors.ListedColormap):
@staticmethod
def _hsv2rgb(hsv):
def _hsv2rgb(hsv: np.ndarray) -> np.ndarray:
"""H(ue) S(aturation) V(alue) to R(red) G(reen) B(lue)."""
return np.array(colorsys.hsv_to_rgb(hsv[0]/360.,hsv[1],hsv[2]))
@staticmethod
def _rgb2hsv(rgb):
def _rgb2hsv(rgb: np.ndarray) -> np.ndarray:
"""R(ed) G(reen) B(lue) to H(ue) S(aturation) V(alue)."""
h,s,v = colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2])
return np.array([h*360,s,v])
@staticmethod
def _hsl2rgb(hsl):
def _hsl2rgb(hsl: np.ndarray) -> np.ndarray:
"""H(ue) S(aturation) L(uminance) to R(red) G(reen) B(lue)."""
return np.array(colorsys.hls_to_rgb(hsl[0]/360.,hsl[2],hsl[1]))
@staticmethod
def _rgb2hsl(rgb):
def _rgb2hsl(rgb: np.ndarray) -> np.ndarray:
"""R(ed) G(reen) B(lue) to H(ue) S(aturation) L(uminance)."""
h,l,s = colorsys.rgb_to_hls(rgb[0],rgb[1],rgb[2])
return np.array([h*360,s,l])
@staticmethod
def _xyz2rgb(xyz):
def _xyz2rgb(xyz: np.ndarray) -> np.ndarray:
"""
CIE Xyz to R(ed) G(reen) B(lue).
@ -483,7 +491,7 @@ class Colormap(mpl.colors.ListedColormap):
return np.clip(rgb,0.,1.)
@staticmethod
def _rgb2xyz(rgb):
def _rgb2xyz(rgb: np.ndarray) -> np.ndarray:
"""
R(ed) G(reen) B(lue) to CIE Xyz.
@ -501,7 +509,7 @@ class Colormap(mpl.colors.ListedColormap):
@staticmethod
def _lab2xyz(lab,ref_white=None):
def _lab2xyz(lab: np.ndarray, ref_white: np.ndarray = None) -> np.ndarray:
"""
CIE Lab to CIE Xyz.
@ -520,7 +528,7 @@ class Colormap(mpl.colors.ListedColormap):
])*(ref_white if ref_white is not None else _ref_white)
@staticmethod
def _xyz2lab(xyz,ref_white=None):
def _xyz2lab(xyz: np.ndarray, ref_white: np.ndarray = None) -> np.ndarray:
"""
CIE Xyz to CIE Lab.
@ -540,7 +548,7 @@ class Colormap(mpl.colors.ListedColormap):
@staticmethod
def _lab2msh(lab):
def _lab2msh(lab: np.ndarray) -> np.ndarray:
"""
CIE Lab to Msh.
@ -558,7 +566,7 @@ class Colormap(mpl.colors.ListedColormap):
])
@staticmethod
def _msh2lab(msh):
def _msh2lab(msh: np.ndarray) -> np.ndarray:
"""
Msh to CIE Lab.
@ -575,29 +583,29 @@ class Colormap(mpl.colors.ListedColormap):
])
@staticmethod
def _lab2rgb(lab):
def _lab2rgb(lab: np.ndarray) -> np.ndarray:
return Colormap._xyz2rgb(Colormap._lab2xyz(lab))
@staticmethod
def _rgb2lab(rgb):
def _rgb2lab(rgb: np.ndarray) -> np.ndarray:
return Colormap._xyz2lab(Colormap._rgb2xyz(rgb))
@staticmethod
def _msh2rgb(msh):
def _msh2rgb(msh: np.ndarray) -> np.ndarray:
return Colormap._lab2rgb(Colormap._msh2lab(msh))
@staticmethod
def _rgb2msh(rgb):
def _rgb2msh(rgb: np.ndarray) -> np.ndarray:
return Colormap._lab2msh(Colormap._rgb2lab(rgb))
@staticmethod
def _hsv2msh(hsv):
def _hsv2msh(hsv: np.ndarray) -> np.ndarray:
return Colormap._rgb2msh(Colormap._hsv2rgb(hsv))
@staticmethod
def _hsl2msh(hsl):
def _hsl2msh(hsl: np.ndarray) -> np.ndarray:
return Colormap._rgb2msh(Colormap._hsl2rgb(hsl))
@staticmethod
def _xyz2msh(xyz):
def _xyz2msh(xyz: np.ndarray) -> np.ndarray:
return Colormap._lab2msh(Colormap._xyz2lab(xyz))

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@ -77,6 +77,12 @@ class TestColormap:
# xyz2msh
assert np.allclose(Colormap._xyz2msh(xyz),msh,atol=1.e-6,rtol=0)
@pytest.mark.parametrize('low,high',[((0,0,0),(1,1,1)),
([0,0,0],[1,1,1])])
def test_from_range_types(self,low,high):
a = Colormap.from_range(low,high)
b = Colormap.from_range(np.array(low),np.array(high))
assert np.all(a.colors == b.colors)
@pytest.mark.parametrize('format',['ASCII','paraview','GOM','gmsh'])
@pytest.mark.parametrize('model',['rgb','hsv','hsl','xyz','lab','msh'])

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@ -4,6 +4,7 @@
!> @details List of files needed by MSC.Marc
!--------------------------------------------------------------------------------------------------
#include "parallelization.f90"
#include "constants.f90"
#include "IO.f90"
#include "YAML_types.f90"
#include "YAML_parse.f90"

15
src/constants.f90 Normal file
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@ -0,0 +1,15 @@
!--------------------------------------------------------------------------------------------------
!> @author Martin Diehl, KU Leuven
!> @brief physical constants
!--------------------------------------------------------------------------------------------------
module constants
use prec
implicit none
public
real(pReal), parameter :: &
T_ROOM = 300.0_pReal, & !< Room temperature in K
kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
end module constants

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@ -5,6 +5,7 @@
!--------------------------------------------------------------------------------------------------
module phase
use prec
use constants
use math
use rotations
use IO

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@ -58,7 +58,7 @@ module function thermalexpansion_init(kinematics_length) result(myKinematics)
associate(prm => param(kinematics_thermal_expansion_instance(p)))
kinematic_type => kinematics%get(k)
prm%T_ref = kinematic_type%get_asFloat('T_ref', defaultVal=0.0_pReal)
prm%T_ref = kinematic_type%get_asFloat('T_ref', defaultVal=T_ROOM)
prm%A(1,1,1) = kinematic_type%get_asFloat('A_11')
prm%A(1,1,2) = kinematic_type%get_asFloat('A_11,T',defaultVal=0.0_pReal)

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@ -7,9 +7,6 @@
!--------------------------------------------------------------------------------------------------
submodule(phase:plastic) dislotungsten
real(pReal), parameter :: &
kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
type :: tParameters
real(pReal) :: &
D = 1.0_pReal, & !< grain size

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@ -9,9 +9,6 @@
!--------------------------------------------------------------------------------------------------
submodule(phase:plastic) dislotwin
real(pReal), parameter :: &
kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
type :: tParameters
real(pReal) :: &
Q_cl = 1.0_pReal, & !< activation energy for dislocation climb
@ -31,7 +28,7 @@ submodule(phase:plastic) dislotwin
delta_G = 1.0_pReal, & !< Free energy difference between austensite and martensite
i_tr = 1.0_pReal, & !< adjustment parameter to calculate MFP for transformation
h = 1.0_pReal, & !< Stack height of hex nucleus
T_ref = 0.0_pReal, &
T_ref = T_ROOM, &
a_cI = 1.0_pReal, &
a_cF = 1.0_pReal
real(pReal), dimension(2) :: &

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@ -19,9 +19,6 @@ submodule(phase:plastic) nonlocal
type(tGeometry), dimension(:), allocatable :: geom
real(pReal), parameter :: &
kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
! storage order of dislocation types
integer, dimension(*), parameter :: &
sgl = [1,2,3,4,5,6,7,8] !< signed (single)