Merge branch 'MiscImprovements' into MoreImprovements

This commit is contained in:
Martin Diehl 2020-01-11 22:37:41 +01:00
commit 3938f34978
4 changed files with 188 additions and 168 deletions

View File

@ -182,8 +182,8 @@ for name in filenames:
nodes = damask.grid_filters.node_coord(size,F)
if options.shape:
centres = damask.grid_filters.cell_coord(size,F)
shapeMismatch = shapeMismatch( size,table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3),nodes,centres)
centers = damask.grid_filters.cell_coord(size,F)
shapeMismatch = shapeMismatch( size,table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3),nodes,centers)
table.add('shapeMismatch(({}))'.format(options.defgrad),
shapeMismatch.reshape((-1,1)),
scriptID+' '+' '.join(sys.argv[1:]))

View File

@ -170,9 +170,18 @@ class Rotation:
################################################################################################
# convert to different orientation representations (numpy arrays)
def asQuaternion(self):
"""Unit quaternion: (q, p_1, p_2, p_3)."""
return self.quaternion.asArray()
def asQuaternion(self,
quaternion = False):
"""
Unit quaternion [q, p_1, p_2, p_3] unless quaternion == True: damask.quaternion object.
Parameters
----------
quaternion : bool, optional
return quaternion as DAMASK object.
"""
return self.quaternion if quaternion else self.quaternion.asArray()
def asEulers(self,
degrees = False):
@ -190,33 +199,36 @@ class Rotation:
return eu
def asAxisAngle(self,
degrees = False):
degrees = False,
pair = False):
"""
Axis angle pair: ([n_1, n_2, n_3], ω).
Axis angle representation [n_1, n_2, n_3, ω] unless pair == True: ([n_1, n_2, n_3], ω).
Parameters
----------
degrees : bool, optional
return rotation angle in degrees.
pair : bool, optional
return tuple of axis and angle.
"""
ax = qu2ax(self.quaternion.asArray())
if degrees: ax[3] = np.degrees(ax[3])
return ax
return (ax[:3],np.degrees(ax[3])) if pair else ax
def asMatrix(self):
"""Rotation matrix."""
return qu2om(self.quaternion.asArray())
def asRodrigues(self,
vector=False):
vector = False):
"""
Rodrigues-Frank vector: ([n_1, n_2, n_3], tan(ω/2)).
Rodrigues-Frank vector representation [n_1, n_2, n_3, tan(ω/2)] unless vector == True: [n_1, n_2, n_3] * tan(ω/2).
Parameters
----------
vector : bool, optional
return as array of length 3, i.e. scale the unit vector giving the rotation axis.
return as actual Rodrigues--Frank vector, i.e. rotation axis scaled by tan(ω/2).
"""
ro = qu2ro(self.quaternion.asArray())
@ -252,8 +264,8 @@ class Rotation:
acceptHomomorph = False,
P = -1):
qu = quaternion if isinstance(quaternion, np.ndarray) and quaternion.dtype == np.dtype(float) \
else np.array(quaternion,dtype=float)
qu = quaternion if isinstance(quaternion, np.ndarray) and quaternion.dtype == np.dtype(float) \
else np.array(quaternion,dtype=float)
if P > 0: qu[1:4] *= -1 # convert from P=1 to P=-1
if qu[0] < 0.0:
if acceptHomomorph:
@ -1193,9 +1205,9 @@ class Orientation:
ref = orientations[0]
for o in orientations:
closest.append(o.equivalentOrientations(
ref.disorientation(o,
SST = False, # select (o[ther]'s) sym orientation
symmetries = True)[2]).rotation) # with lowest misorientation
ref.disorientation(o,
SST = False, # select (o[ther]'s) sym orientation
symmetries = True)[2]).rotation) # with lowest misorientation
return Orientation(Rotation.fromAverage(closest,weights),ref.lattice)

View File

@ -296,7 +296,7 @@ end subroutine readGeom
!---------------------------------------------------------------------------------------------------
!> @brief Calculate undeformed position of IPs/cell centres (pretend to be an element)
!> @brief Calculate undeformed position of IPs/cell centers (pretend to be an element)
!---------------------------------------------------------------------------------------------------
function IPcoordinates0(grid,geomSize,grid3Offset)

View File

@ -1,37 +1,9 @@
! ###################################################################
! Copyright (c) 2013-2015, Marc De Graef/Carnegie Mellon University
! Modified 2017-2019, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
! All rights reserved.
!
! Redistribution and use in source and binary forms, with or without modification, are
! permitted provided that the following conditions are met:
!
! - Redistributions of source code must retain the above copyright notice, this list
! of conditions and the following disclaimer.
! - Redistributions in binary form must reproduce the above copyright notice, this
! list of conditions and the following disclaimer in the documentation and/or
! other materials provided with the distribution.
! - Neither the names of Marc De Graef, Carnegie Mellon University nor the names
! of its contributors may be used to endorse or promote products derived from
! this software without specific prior written permission.
!
! THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
! AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
! IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
! ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
! LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
! DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
! SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
! CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
! OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
! USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
! ###################################################################
!---------------------------------------------------------------------------------------------------
!> @author Marc De Graef, Carnegie Mellon University
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!> @author Philip Eisenlohr, Michigan State University
!> @brief general quaternion math, not limited to unit quaternions
!> @details w is the real part, (x, y, z) are the imaginary parts.
!> @details w is the real part, (x, y, z) are the imaginary parts.
!> @details https://en.wikipedia.org/wiki/Quaternion
!---------------------------------------------------------------------------------------------------
module quaternions
use prec
@ -78,15 +50,16 @@ module quaternions
procedure, public :: abs__
procedure, public :: dot_product__
procedure, public :: conjg__
procedure, public :: exp__
procedure, public :: log__
procedure, public :: homomorphed => quat_homomorphed
procedure, public :: asArray
procedure, public :: conjg => conjg__
procedure, public :: real => real__
procedure, public :: aimag => aimag__
procedure, public :: homomorphed
procedure, public :: asArray
procedure, public :: inverse
end type
interface assignment (=)
@ -118,6 +91,14 @@ module quaternions
module procedure log__
end interface log
interface real
module procedure real__
end interface real
interface aimag
module procedure aimag__
end interface aimag
private :: &
unitTest
@ -125,49 +106,46 @@ contains
!--------------------------------------------------------------------------------------------------
!> @brief doing self test
!> @brief do self test
!--------------------------------------------------------------------------------------------------
subroutine quaternions_init
write(6,'(/,a)') ' <<<+- quaternions init -+>>>'
write(6,'(/,a)') ' <<<+- quaternions init -+>>>'; flush(6)
call unitTest
end subroutine quaternions_init
!---------------------------------------------------------------------------------------------------
!> constructor for a quaternion from a 4-vector
!> construct a quaternion from a 4-vector
!---------------------------------------------------------------------------------------------------
type(quaternion) pure function init__(array)
real(pReal), intent(in), dimension(4) :: array
init__%w=array(1)
init__%x=array(2)
init__%y=array(3)
init__%z=array(4)
init__%w = array(1)
init__%x = array(2)
init__%y = array(3)
init__%z = array(4)
end function init__
!---------------------------------------------------------------------------------------------------
!> assing a quaternion
!> assign a quaternion
!---------------------------------------------------------------------------------------------------
elemental pure subroutine assign_quat__(self,other)
type(quaternion), intent(out) :: self
type(quaternion), intent(in) :: other
self%w = other%w
self%x = other%x
self%y = other%y
self%z = other%z
self = [other%w,other%x,other%y,other%z]
end subroutine assign_quat__
!---------------------------------------------------------------------------------------------------
!> assing a 4-vector
!> assign a 4-vector
!---------------------------------------------------------------------------------------------------
pure subroutine assign_vec__(self,other)
@ -183,67 +161,57 @@ end subroutine assign_vec__
!---------------------------------------------------------------------------------------------------
!> addition of two quaternions
!> add a quaternion
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function add__(self,other)
class(quaternion), intent(in) :: self,other
add__%w = self%w + other%w
add__%x = self%x + other%x
add__%y = self%y + other%y
add__%z = self%z + other%z
add__ = [ self%w, self%x, self%y ,self%z] &
+ [other%w, other%x, other%y,other%z]
end function add__
!---------------------------------------------------------------------------------------------------
!> unary positive operator
!> return (unary positive operator)
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function pos__(self)
class(quaternion), intent(in) :: self
pos__%w = self%w
pos__%x = self%x
pos__%y = self%y
pos__%z = self%z
pos__ = self * (+1.0_pReal)
end function pos__
!---------------------------------------------------------------------------------------------------
!> subtraction of two quaternions
!> subtract a quaternion
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function sub__(self,other)
class(quaternion), intent(in) :: self,other
sub__%w = self%w - other%w
sub__%x = self%x - other%x
sub__%y = self%y - other%y
sub__%z = self%z - other%z
sub__ = [ self%w, self%x, self%y ,self%z] &
- [other%w, other%x, other%y,other%z]
end function sub__
!---------------------------------------------------------------------------------------------------
!> unary positive operator
!> negate (unary negative operator)
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function neg__(self)
class(quaternion), intent(in) :: self
neg__%w = -self%w
neg__%x = -self%x
neg__%y = -self%y
neg__%z = -self%z
neg__ = self * (-1.0_pReal)
end function neg__
!---------------------------------------------------------------------------------------------------
!> multiplication of two quaternions
!> multiply with a quaternion
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function mul_quat__(self,other)
@ -258,23 +226,20 @@ end function mul_quat__
!---------------------------------------------------------------------------------------------------
!> multiplication of quaternions with scalar
!> multiply with a scalar
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function mul_scal__(self,scal)
class(quaternion), intent(in) :: self
real(pReal), intent(in) :: scal
real(pReal), intent(in) :: scal
mul_scal__%w = self%w*scal
mul_scal__%x = self%x*scal
mul_scal__%y = self%y*scal
mul_scal__%z = self%z*scal
mul_scal__ = [self%w,self%x,self%y,self%z]*scal
end function mul_scal__
!---------------------------------------------------------------------------------------------------
!> division of two quaternions
!> divide by a quaternion
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function div_quat__(self,other)
@ -286,12 +251,12 @@ end function div_quat__
!---------------------------------------------------------------------------------------------------
!> divisiont of quaternions by scalar
!> divide by a scalar
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function div_scal__(self,scal)
class(quaternion), intent(in) :: self
real(pReal), intent(in) :: scal
real(pReal), intent(in) :: scal
div_scal__ = [self%w,self%x,self%y,self%z]/scal
@ -299,7 +264,7 @@ end function div_scal__
!---------------------------------------------------------------------------------------------------
!> equality of two quaternions
!> test equality
!---------------------------------------------------------------------------------------------------
logical elemental pure function eq__(self,other)
@ -312,7 +277,7 @@ end function eq__
!---------------------------------------------------------------------------------------------------
!> inequality of two quaternions
!> test inequality
!---------------------------------------------------------------------------------------------------
logical elemental pure function neq__(self,other)
@ -324,20 +289,7 @@ end function neq__
!---------------------------------------------------------------------------------------------------
!> quaternion to the power of a scalar
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function pow_scal__(self,expon)
class(quaternion), intent(in) :: self
real(pReal), intent(in) :: expon
pow_scal__ = exp(log(self)*expon)
end function pow_scal__
!---------------------------------------------------------------------------------------------------
!> quaternion to the power of a quaternion
!> raise to the power of a quaternion
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function pow_quat__(self,expon)
@ -350,45 +302,60 @@ end function pow_quat__
!---------------------------------------------------------------------------------------------------
!> exponential of a quaternion
!> ToDo: Lacks any check for invalid operations
!> raise to the power of a scalar
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function pow_scal__(self,expon)
class(quaternion), intent(in) :: self
real(pReal), intent(in) :: expon
pow_scal__ = exp(log(self)*expon)
end function pow_scal__
!---------------------------------------------------------------------------------------------------
!> take exponential
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function exp__(self)
class(quaternion), intent(in) :: self
real(pReal) :: absImag
absImag = norm2([self%x, self%y, self%z])
absImag = norm2(aimag(self))
exp__ = exp(self%w) * [ cos(absImag), &
self%x/absImag * sin(absImag), &
self%y/absImag * sin(absImag), &
self%z/absImag * sin(absImag)]
exp__ = merge(exp(self%w) * [ cos(absImag), &
self%x/absImag * sin(absImag), &
self%y/absImag * sin(absImag), &
self%z/absImag * sin(absImag)], &
IEEE_value(1.0_pReal,IEEE_SIGNALING_NAN), &
dNeq0(absImag))
end function exp__
!---------------------------------------------------------------------------------------------------
!> logarithm of a quaternion
!> ToDo: Lacks any check for invalid operations
!> take logarithm
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function log__(self)
class(quaternion), intent(in) :: self
real(pReal) :: absImag
absImag = norm2([self%x, self%y, self%z])
absImag = norm2(aimag(self))
log__ = [log(abs(self)), &
self%x/absImag * acos(self%w/abs(self)), &
self%y/absImag * acos(self%w/abs(self)), &
self%z/absImag * acos(self%w/abs(self))]
log__ = merge([log(abs(self)), &
self%x/absImag * acos(self%w/abs(self)), &
self%y/absImag * acos(self%w/abs(self)), &
self%z/absImag * acos(self%w/abs(self))], &
IEEE_value(1.0_pReal,IEEE_SIGNALING_NAN), &
dNeq0(absImag))
end function log__
!---------------------------------------------------------------------------------------------------
!> norm of a quaternion
!> return norm
!---------------------------------------------------------------------------------------------------
real(pReal) elemental pure function abs__(a)
@ -400,7 +367,7 @@ end function abs__
!---------------------------------------------------------------------------------------------------
!> dot product of two quaternions
!> calculate dot product
!---------------------------------------------------------------------------------------------------
real(pReal) elemental pure function dot_product__(a,b)
@ -412,31 +379,31 @@ end function dot_product__
!---------------------------------------------------------------------------------------------------
!> conjugate complex of a quaternion
!> take conjugate complex
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function conjg__(a)
class(quaternion), intent(in) :: a
conjg__ = quaternion([a%w, -a%x, -a%y, -a%z])
conjg__ = [a%w, -a%x, -a%y, -a%z]
end function conjg__
!---------------------------------------------------------------------------------------------------
!> homomorphed quaternion of a quaternion
!> homomorph
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function quat_homomorphed(self)
type(quaternion) elemental pure function homomorphed(self)
class(quaternion), intent(in) :: self
quat_homomorphed = quaternion(-[self%w,self%x,self%y,self%z])
homomorphed = - self
end function quat_homomorphed
end function homomorphed
!---------------------------------------------------------------------------------------------------
!> quaternion as plain array
!> return as plain array
!---------------------------------------------------------------------------------------------------
pure function asArray(self)
@ -449,7 +416,7 @@ end function asArray
!---------------------------------------------------------------------------------------------------
!> real part of a quaternion
!> real part (scalar)
!---------------------------------------------------------------------------------------------------
pure function real__(self)
@ -462,7 +429,7 @@ end function real__
!---------------------------------------------------------------------------------------------------
!> imaginary part of a quaternion
!> imaginary part (3-vector)
!---------------------------------------------------------------------------------------------------
pure function aimag__(self)
@ -474,45 +441,86 @@ pure function aimag__(self)
end function aimag__
!---------------------------------------------------------------------------------------------------
!> inverse
!---------------------------------------------------------------------------------------------------
type(quaternion) elemental pure function inverse(self)
class(quaternion), intent(in) :: self
inverse = conjg(self)/abs(self)**2.0_pReal
end function inverse
!--------------------------------------------------------------------------------------------------
!> @brief check correctness of (some) quaternions functions
!--------------------------------------------------------------------------------------------------
subroutine unitTest
real(pReal), dimension(4) :: qu
type(quaternion) :: q, q_2
call random_number(qu)
q = qu
qu = (qu-0.5_pReal) * 2.0_pReal
q = quaternion(qu)
q_2= qu
if(any(dNeq(q%asArray(),q_2%asArray()))) call IO_error(401,ext_msg='assign_vec__')
q_2 = q + q
if(any(dNeq(q_2%asArray(),2.0_pReal*qu))) call IO_error(401,ext_msg='add__')
if(any(dNeq(q_2%asArray(),2.0_pReal*qu))) call IO_error(401,ext_msg='add__')
q_2 = q - q
if(any(dNeq0(q_2%asArray()))) call IO_error(401,ext_msg='sub__')
if(any(dNeq0(q_2%asArray()))) call IO_error(401,ext_msg='sub__')
q_2 = q * 5.0_preal
if(any(dNeq(q_2%asArray(),5.0_pReal*qu))) call IO_error(401,ext_msg='mul__')
q_2 = q * 5.0_pReal
if(any(dNeq(q_2%asArray(),5.0_pReal*qu))) call IO_error(401,ext_msg='mul__')
q_2 = q / 0.5_preal
if(any(dNeq(q_2%asArray(),2.0_pReal*qu))) call IO_error(401,ext_msg='div__')
q_2 = q / 0.5_pReal
if(any(dNeq(q_2%asArray(),2.0_pReal*qu))) call IO_error(401,ext_msg='div__')
q_2 = q * 0.3_pReal
if(dNeq0(abs(q)) .and. q_2 == q) call IO_error(401,ext_msg='eq__')
q_2 = q
if(q_2 /= q) call IO_error(401,ext_msg='eq__')
if(q_2 /= q) call IO_error(401,ext_msg='neq__')
if(any(dNeq(q%asArray(),qu))) call IO_error(401,ext_msg='eq__')
if(dNeq(q%real(), qu(1))) call IO_error(401,ext_msg='real()')
if(any(dNeq(q%aimag(), qu(2:4)))) call IO_error(401,ext_msg='aimag()')
if(dNeq(abs(q),norm2(qu))) call IO_error(401,ext_msg='abs__')
if(dNeq(abs(q)**2.0_pReal, real(q*q%conjg()),1.0e-14_pReal)) &
call IO_error(401,ext_msg='abs__/*conjg')
if(any(dNeq(q%asArray(),qu))) call IO_error(401,ext_msg='eq__')
if(dNeq(q%real(), qu(1))) call IO_error(401,ext_msg='real()')
if(any(dNeq(q%aimag(), qu(2:4)))) call IO_error(401,ext_msg='aimag()')
q_2 = q%homomorphed()
if(q /= q_2* (-1.0_pReal)) call IO_error(401,ext_msg='homomorphed')
if(dNeq(q_2%real(), qu(1)* (-1.0_pReal))) call IO_error(401,ext_msg='homomorphed/real')
if(any(dNeq(q_2%aimag(),qu(2:4)*(-1.0_pReal)))) call IO_error(401,ext_msg='homomorphed/aimag')
if(q /= q_2* (-1.0_pReal)) call IO_error(401,ext_msg='homomorphed')
if(dNeq(q_2%real(), qu(1)* (-1.0_pReal))) call IO_error(401,ext_msg='homomorphed/real')
if(any(dNeq(q_2%aimag(),qu(2:4)*(-1.0_pReal)))) call IO_error(401,ext_msg='homomorphed/aimag')
q_2 = conjg(q)
if(dNeq(q_2%real(), q%real())) call IO_error(401,ext_msg='conjg/real')
if(any(dNeq(q_2%aimag(),q%aimag()*(-1.0_pReal)))) call IO_error(401,ext_msg='conjg/aimag')
if(dNeq(abs(q),abs(q_2))) call IO_error(401,ext_msg='conjg/abs')
if(q /= conjg(q_2)) call IO_error(401,ext_msg='conjg/involution')
if(dNeq(q_2%real(), q%real())) call IO_error(401,ext_msg='conjg/real')
if(any(dNeq(q_2%aimag(),q%aimag()*(-1.0_pReal)))) call IO_error(401,ext_msg='conjg/aimag')
if(abs(q) > 0.0_pReal) then
q_2 = q * q%inverse()
if( dNeq(real(q_2), 1.0_pReal,1.0e-15_pReal)) call IO_error(401,ext_msg='inverse/real')
if(any(dNeq0(aimag(q_2), 1.0e-15_pReal))) call IO_error(401,ext_msg='inverse/aimag')
q_2 = q/abs(q)
q_2 = conjg(q_2) - inverse(q_2)
if(any(dNeq0(q_2%asArray(),1.0e-15_pReal))) call IO_error(401,ext_msg='inverse/conjg')
endif
#if !(defined(__GFORTRAN__) && __GNUC__ < 9)
if (norm2(aimag(q)) > 0.0_pReal) then
if (dNeq0(abs(q-exp(log(q))),1.0e-13_pReal)) call IO_error(401,ext_msg='exp/log')
if (dNeq0(abs(q-log(exp(q))),1.0e-13_pReal)) call IO_error(401,ext_msg='log/exp')
endif
#endif
end subroutine unitTest