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Merge branch 'development' into fix_homogenization_restart

This commit is contained in:
Vitesh Shah 2021-02-25 09:50:38 +01:00
parent c383482405 9436edbd85
commit 0d0aaa0df6
37 changed files with 311 additions and 417 deletions
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6
DAMASK_prerequisites.sh
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@ -84,7 +84,7 @@ for executable in python python3; do
done
secondLevel "Details on $DEFAULT_PYTHON:"
echo $(ls -la $(which $DEFAULT_PYTHON))
for module in numpy scipy pandas;do
for module in numpy scipy pandas matplotlib yaml h5py;do
thirdLevel $module
$DEFAULT_PYTHON -c "import $module; \
print('Version: {}'.format($module.__version__)); \
@ -94,10 +94,6 @@ thirdLevel vtk
$DEFAULT_PYTHON -c "import vtk; \
print('Version: {}'.format(vtk.vtkVersion.GetVTKVersion())); \
print('Location: {}'.format(vtk.__file__))"
thirdLevel h5py
$DEFAULT_PYTHON -c "import h5py; \
print('Version: {}'.format(h5py.version.version)); \
print('Location: {}'.format(h5py.__file__))"
firstLevel "GNU Compiler Collection"
for executable in gcc g++ gfortran ;do

2
VERSION
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@ -1 +1 @@
v3.0.0-alpha2-478-gc9e4dc21f
v3.0.0-alpha2-530-g0d0226f70

8
examples/ConfigFiles/Homogenization_multiField.config
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@ -1,8 +0,0 @@
[SX]
type isostrain
Ngrains 1
{./Homogenization_Damage_NonLocal.config}
{./Homogenization_Thermal_Conduction.config}
{./Homogenization_VacancyFlux_CahnHilliard.config}
{./Homogenization_Porosity_PhaseField.config}
{./Homogenization_HydrogenFlux_CahnHilliard.config}

6
examples/ConfigFiles/Phase_Isotropic_AluminumIsotropic.yaml
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@ -1,9 +1,9 @@
# Kuo, J. C., Mikrostrukturmechanik von Bikristallen mit Kippkorngrenzen. Shaker-Verlag 2004. http://edoc.mpg.de/204079
Aluminum:
mechanics:
lattice: aP
elasticity: {C_11: 110.9e9, C_12: 58.34e9, type: hooke}
output: [F, P, Fe, Fp, Lp]
mechanics:
output: [F, P, F_e, F_p, L_p]
elasticity: {type: hooke, C_11: 110.9e9, C_12: 58.34e9}
plasticity:
type: isotropic
output: [xi]

9
examples/ConfigFiles/Phase_Isotropic_FreeSurface.yaml
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@ -1,9 +1,8 @@
# Maiti and Eisenlohr 2018 Scripta Materialia
Air:
mechanics:
lattice: aP
elasticity: {C_11: 10e9, C_12: 0.0, type: hooke}
output: [F, P, Fe, Fp, Lp]
mechanics:
output: [F, P, F_e, F_p, L_p]
elasticity: {type: hooke, C_11: 1e8, C_12: 1e6}
plasticity:
type: isotropic
output: [xi]
@ -14,4 +13,4 @@ Air:
M: 3
h_0: 1e6
a: 2
dilatation: true
dilatation: True

21
examples/ConfigFiles/Phase_Phenopowerlaw_Aluminum.config
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@ -1,21 +0,0 @@
[Aluminum]
elasticity hooke
plasticity phenopowerlaw
(output) resistance_slip
(output) accumulatedshear_slip
lattice_structure fcc
Nslip 12 # per family
c11 106.75e9
c12 60.41e9
c44 28.34e9
gdot0_slip 0.001
n_slip 20
tau0_slip 31e6 # per family
tausat_slip 63e6 # per family
a_slip 2.25
h0_slipslip 75e6
interaction_slipslip 1 1 1.4 1.4 1.4 1.4

16
examples/ConfigFiles/Phase_Phenopowerlaw_Aluminum.yaml Normal file
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@ -0,0 +1,16 @@
Aluminum:
lattice: cF
mechanics:
output: [F, P, F_e, F_p, L_p, O]
elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
plasticity:
N_sl: [12]
a_sl: 2.25
dot_gamma_0_sl: 0.001
h_0_sl_sl: 75e6
h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4]
n_sl: 20
output: [xi_sl, gamma_sl]
type: phenopowerlaw
xi_0_sl: [31e6]
xi_inf_sl: [63e6]

2
examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Ferrite.yaml
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@ -2,8 +2,8 @@
# Tasan et.al. 2015 International Journal of Plasticity
# Diehl et.al. 2015 Meccanica
Ferrite:
mechanics:
lattice: cI
mechanics:
elasticity: {C_11: 233.3e9, C_12: 135.5e9, C_44: 118.0e9, type: hooke}
plasticity:
N_sl: [12, 12]

2
examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.yaml
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@ -2,8 +2,8 @@
# Tasan et.al. 2015 International Journal of Plasticity
# Diehl et.al. 2015 Meccanica
Martensite:
mechanics:
lattice: cI
mechanics:
elasticity: {C_11: 417.4e9, C_12: 242.4e9, C_44: 211.1e9, type: hooke}
plasticity:
N_sl: [12, 12]

27
examples/ConfigFiles/Phase_Phenopowerlaw_Gold.config
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@ -1,27 +0,0 @@
# parameters fitted by D. Ma to:
# I. Kovács, G. Vörös
# On the mathematical description of the tensile stress-strain curves of polycrystalline face centered cubic metals
# International Journal of Plasticity, Volume 12, Issue 1, 1996, Pages 35–43
# DOI: 10.1016/S0749-6419(95)00043-7
[gold_phenopowerlaw]
elasticity hooke
plasticity phenopowerlaw
(output) resistance_slip
lattice_structure fcc
Nslip 12 # per family
c11 191.0e9
c12 162.0e9
c44 42.20e9
gdot0_slip 0.001
n_slip 83.3
tau0_slip 26.25e6 # per family
tausat_slip 53.00e6 # per family
a_slip 1.0
h0_slipslip 75e6
interaction_slipslip 1 1 1.4 1.4 1.4 1.4

21
examples/ConfigFiles/Phase_Phenopowerlaw_Gold.yaml Normal file
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@ -0,0 +1,21 @@
# parameters fitted by D. Ma to:
# On the mathematical description of the tensile stress-strain curves of polycrystalline face centered cubic metals
# International Journal of Plasticity, Volume 12, Issue 1, 1996, Pages 35-43
# DOI: 10.1016/S0749-6419(95)00043-7
Gold:
lattice: cF
mechanics:
output: [F, P, F_e, F_p, L_p, O]
elasticity: {type: hooke, C_11: 191e9, C_12: 162e9, C_44: 42.2e9}
plasticity:
type: phenopowerlaw
output: [xi_sl]
N_sl: [12]
n_sl: 83
dot_gamma_0_sl: 0.001
h_0_sl_sl: 75e6
h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4]
a_sl: 1.0
xi_0_sl: [26e6]
xi_inf_sl: [53e6]

56
examples/ConfigFiles/Phase_Phenopowerlaw_Magnesium.config
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@ -1,56 +0,0 @@
#-------------------#
<phase>
#-------------------#
/echo/
[Mg]
plasticity phenopowerlaw
elasticity hooke
(output) resistance_slip
(output) resistance_twin
lattice_structure hex
c/a 1.62350 # from Tromans 2011, Elastic Anisotropy of HCP Metal Crystals and Polycrystals
c11 59.3e9 # - " -
c33 61.5e9 # - " -
c44 16.4e9 # - " -
c12 25.7e9 # - " -
c13 21.4e9 # - " -
# basal prism prism pyr(a) pyr(c+a) pyr(c+a)
Nslip 3 3 0 6 0 6 # from Agnew et al 2006, Validating a polycrystal model for the elastoplastic response of mg alloy AZ32 using in situ neutron diffraction
# T1 C1 T2 C2
Ntwin 6 0 0 6 # - " -
# basal prism prism pyr(a) pyr(c+a) pyr(c+a)
tau0_slip 10.0e6 55.0e6 0 60.0e6 0.0 60.0e6 # - " - table 1, pyr(a) set to pyr(c+a)
tausat_slip 40.0e6 135.0e6 0 150.0e6 0.0 150.0e6 # - " - table 1, pyr(a) set to pyr(c+a)
# T1 C1 T2 C2
tau0_twin 40e6 0.0 0.0 60.0e6 # - " - table 1, compressive twin guessed by Steffi, tensile twin modified to match experimental results
h0_twintwin 50.0e6 # - " - table 1, same range as theta_0
h0_slipslip 500.0e6 # - " - table 1, same range as theta_0
h0_twinslip 150.0e6 # guessing
interaction_slipslip 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 # just guessing
interaction_twintwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 # - " -
interaction_sliptwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 # - " -
interaction_twinslip 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 # - " -
####################################################
# open for discussion
####################################################
n_twin 20
n_slip 20
gdot0_twin 0.001
gdot0_slip 0.001
twin_b 0
twin_c 0
twin_d 20
twin_e 20
a_slip 2.25
s_pr 10.0 # push-up factor for slip saturation due to twinning

31
examples/ConfigFiles/Phase_Phenopowerlaw_Magnesium.yaml Normal file
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@ -0,0 +1,31 @@
# Tromans 2011, Elastic Anisotropy of HCP Metal Crystals and Polycrystals
Magnesium:
lattice: hP
c/a: 1.62350
mechanics:
output: [F, P, F_e, F_p, L_p, O]
elasticity: {C_11: 59.3e9, C_12: 25.7e9, C_13: 21.4e9, C_33: 61.5e9, C_44: 16.4e9, type: hooke}
plasticity:
N_sl: [3, 3, 0, 6, 0, 6]
N_tw: [6, 0, 0, 6]
h_0_tw_tw: 50.0e6
h_0_sl_sl: 500.0e6
h_0_tw_sl: 150.0e6
h_sl_sl: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
h_tw_tw: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
h_sl_tw: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
h_tw_sl: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
output: [xi_sl, xi_tw]
type: phenopowerlaw
xi_0_sl: [10.0e6, 55.0e6, 0, 60.0e6, 0.0, 60.0e6]
xi_inf_sl: [40.0e6, 135.0e6, 0, 150.0e6, 0.0, 150.0e6]
xi_0_tw: [40e6, 0.0, 0.0, 60.0e6]
####################################################
# open for discussion
####################################################
a_sl: 2.25
dot_gamma_0_sl: 0.001
dot_gamma_0_tw: 0.001
n_sl: 20
n_tw: 20
f_sl_sat_tw: 10.0

23
examples/ConfigFiles/Phase_Phenopowerlaw_cpTi-alpha.config
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@ -1,23 +0,0 @@
[cpTi-alpha]
plasticity phenopowerlaw
elasticity hooke
lattice_structure hex
covera_ratio 1.587
# M. Levy, Handbook of Elastic Properties of Solids, Liquids, and Gases (2001)
c11 160.0e9
c12 90.0e9
c13 66.0e9
c33 181.7e9
c44 46.5e9
# C. Zambaldi, "Orientation informed nanoindentation of a-titanium: Indentation pileup in hexagonal metals deforming by prismatic slip", J. Mater. Res., Vol. 27, No. 1, Jan 14, 2012
gdot0_slip 0.001
n_slip 20
nslip 3 3 0 6
tau0_slip 349.3e6 150e6 0 1107.9e6
tausat_slip 568.6e6 1502.2e6 0 3420.1e6
a_slip 2
h0_slipslip 15e6
interaction_slipslip 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

19
examples/ConfigFiles/Phase_Phenopowerlaw_cpTi.yaml Normal file
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@ -0,0 +1,19 @@
# M. Levy, Handbook of Elastic Properties of Solids, Liquids, and Gases (2001)
# C. Zambaldi, "Orientation informed nanoindentation of a-titanium: Indentation pileup in hexagonal metals deforming by prismatic slip", J. Mater. Res., Vol. 27, No. 1, Jan 14, 2012
Ti-alpha:
lattice: hP
c/a: 1.587
mechanics:
output: [F, P, F_e, F_p, L_p, O]
elasticity: {C_11: 160.0e9, C_12: 90.0e9, C_13: 66.0e9, C_33: 181.7e9, C_44: 46.5e9, type: hooke}
plasticity:
N_sl: [3, 3, 0, 0, 12]
a_sl: 2.0
dot_gamma_0_sl: 0.001
h_0_sl_sl: 200e6
h_sl_sl: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
n_sl: 20
output: [gamma_sl]
type: phenopowerlaw
xi_0_sl: [349e6, 150e6, 0, 0, 1107e6]
xi_inf_sl: [568e6, 1502e6, 0, 0, 3420e6]

2
examples/ConfigFiles/Texture_Gauss_001.config
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@ -1,2 +0,0 @@
[001]
(gauss) phi1 0.000 Phi 0.000 phi2 0.000

2
examples/ConfigFiles/Texture_Gauss_101.config
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@ -1,2 +0,0 @@
[101]
(gauss) phi1 0.000 Phi 45.000 phi2 90.000

2
examples/ConfigFiles/Texture_Gauss_111.config
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@ -1,2 +0,0 @@
[111]
(gauss) phi1 0.000 Phi 54.7356 phi2 45.000

2
examples/ConfigFiles/Texture_Gauss_123.config
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@ -1,2 +0,0 @@
[123]
(gauss) phi1 209.805 Phi 29.206 phi2 63.435

20
examples/ConfigFiles/material.config
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@ -1,20 +0,0 @@
# The material.config file needs to specify five parts:
# homogenization, microstructure, crystallite, phase, and texture.
# You can either put the full text in here or include suited separate files
<homogenization>
{./Homogenization_Isostrain_SX.config}
<microstructure>
[one_only]
crystallite 1
(constituent) phase 1 texture 1 fraction 1.0
<crystallite>
{./Crystallite_All.config}
<phase>
{./Phase_Phenopowerlaw_Aluminum.config}
<texture>
{./Texture_Gauss_001.config}

156
python/damask/_configmaterial.py
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@ -3,6 +3,7 @@ import numpy as np
from . import Config
from . import Rotation
from . import Orientation
from . import util
class ConfigMaterial(Config):
"""Material configuration."""
@ -46,7 +47,7 @@ class ConfigMaterial(Config):
@staticmethod
def from_table(table,constituents={},**kwargs):
def from_table(table,**kwargs):
"""
Load from an ASCII table.
@ -54,12 +55,9 @@ class ConfigMaterial(Config):
----------
table : damask.Table
Table that contains material information.
constituents : dict, optional
Entries for 'constituents'. The key is the name and the value specifies
the label of the data column in the table
**kwargs
Keyword arguments where the key is the name and the value specifies
the label of the data column in the table
the label of the data column in the table.
Examples
--------
@ -70,7 +68,8 @@ class ConfigMaterial(Config):
pos pos pos qu qu qu qu phase homog
0 0 0 0 0.19 0.8 0.24 -0.51 Aluminum SX
1 1 0 0 0.8 0.19 0.24 -0.51 Steel SX
>>> cm.from_table(t,{'O':'qu','phase':'phase'},homogenization='homog')
1 1 1 0 0.8 0.19 0.24 -0.51 Steel SX
>>> cm.from_table(t,O='qu',phase='phase',homogenization='homog')
material:
- constituents:
- O: [0.19, 0.8, 0.24, -0.51]
@ -86,16 +85,13 @@ class ConfigMaterial(Config):
phase: {}
"""
constituents_ = {k:table.get(v) for k,v in constituents.items()}
kwargs_ = {k:table.get(v) for k,v in kwargs.items()}
_,idx = np.unique(np.hstack(list({**constituents_,**kwargs_}.values())),return_index=True,axis=0)
_,idx = np.unique(np.hstack(list(kwargs_.values())),return_index=True,axis=0)
idx = np.sort(idx)
constituents_ = {k:np.atleast_1d(v[idx].squeeze()) for k,v in constituents_.items()}
kwargs_ = {k:np.atleast_1d(v[idx].squeeze()) for k,v in kwargs_.items()}
return ConfigMaterial().material_add(constituents_,**kwargs_)
return ConfigMaterial().material_add(**kwargs_)
@property
@ -103,7 +99,6 @@ class ConfigMaterial(Config):
"""Check for completeness."""
ok = True
for top_level in ['homogenization','phase','material']:
# ToDo: With python 3.8 as prerequisite we can shorten with :=
ok &= top_level in self
if top_level not in self: print(f'{top_level} entry missing')
@ -154,7 +149,7 @@ class ConfigMaterial(Config):
@property
def is_valid(self):
"""Check for valid file layout."""
"""Check for valid content."""
ok = True
if 'phase' in self:
@ -163,8 +158,7 @@ class ConfigMaterial(Config):
try:
Orientation(lattice=v['lattice'])
except KeyError:
s = v['lattice']
print(f"Invalid lattice: '{s}' in phase '{k}'")
print(f"Invalid lattice '{v['lattice']}' in phase '{k}'")
ok = False
if 'material' in self:
@ -172,16 +166,15 @@ class ConfigMaterial(Config):
if 'constituents' in m:
v = 0.0
for c in m['constituents']:
v+= float(c['v'])
v += float(c['v'])
if 'O' in c:
try:
Rotation.from_quaternion(c['O'])
except ValueError:
o = c['O']
print(f"Invalid orientation: '{o}' in material '{i}'")
print(f"Invalid orientation '{c['O']}' in material '{i}'")
ok = False
if not np.isclose(v,1.0):
print(f"Invalid total fraction (v) '{v}' in material '{i}'")
print(f"Total fraction v = {v} ≠ 1 in material '{i}'")
ok = False
return ok
@ -200,10 +193,15 @@ class ConfigMaterial(Config):
constituent: list of ints, optional
Limit renaming to selected constituents.
Returns
-------
cfg : damask.ConfigMaterial
Updated material configuration.
"""
dup = self.copy()
for i,m in enumerate(dup['material']):
if ID and i not in ID: continue
if ID is not None and i not in ID: continue
for c in m['constituents']:
if constituent is not None and c not in constituent: continue
try:
@ -224,10 +222,15 @@ class ConfigMaterial(Config):
ID: list of ints, optional
Limit renaming to selected homogenization IDs.
Returns
-------
cfg : damask.ConfigMaterial
Updated material configuration.
"""
dup = self.copy()
for i,m in enumerate(dup['material']):
if ID and i not in ID: continue
if ID is not None and i not in ID: continue
try:
m['homogenization'] = mapping[m['homogenization']]
except KeyError:
@ -235,24 +238,27 @@ class ConfigMaterial(Config):
return dup
def material_add(self,constituents=None,**kwargs):
def material_add(self,**kwargs):
"""
Add material entries.
Parameters
----------
constituents : dict, optional
Entries for 'constituents' as key-value pair.
**kwargs
Key-value pairs.
Returns
-------
cfg : damask.ConfigMaterial
Updated material configuration.
Examples
--------
>>> import numpy as np
>>> import damask
>>> O = damask.Rotation.from_random(3).as_quaternion()
>>> phase = ['Aluminum','Steel','Aluminum']
>>> m = damask.ConfigMaterial().material_add(constituents={'phase':phase,'O':O},
... homogenization='SX')
>>> m = damask.ConfigMaterial().material_add(phase = ['Aluminum','Steel'],
... O = damask.Rotation.from_random(2),
... homogenization = 'SX')
>>> m
material:
- constituents:
@ -265,63 +271,59 @@ class ConfigMaterial(Config):
v: 1.0
phase: Steel
homogenization: SX
homogenization: {}
phase: {}
>>> m = damask.ConfigMaterial().material_add(phase = np.array(['Austenite','Martensite']).reshape(1,2),
... O = damask.Rotation.from_random((2,2)),
... v = np.array([0.2,0.8]).reshape(1,2),
... homogenization = ['A','B'])
>>> m
material:
- constituents:
- O: [0.0886257, -0.144848, 0.615674, -0.769487]
v: 1.0
phase: Aluminum
homogenization: SX
- phase: Austenite
O: [0.659802978293224, 0.6953785848195171, 0.22426295326327111, -0.17554139512785227]
v: 0.2
- phase: Martensite
O: [0.49356745891301596, 0.2841806579193434, -0.7487679215072818, -0.339085707289975]
v: 0.8
homogenization: A
- constituents:
- phase: Austenite
O: [0.26542221365204055, 0.7268854930702071, 0.4474726435701472, -0.44828201137283735]
v: 0.2
- phase: Martensite
O: [0.6545817158479885, -0.08004812803625233, -0.6226561293931374, 0.4212059104577611]
v: 0.8
homogenization: B
homogenization: {}
phase: {}
"""
length = -1
for v in kwargs.values():
if hasattr(v,'__len__') and not isinstance(v,str):
if length != -1 and len(v) != length:
raise ValueError('Cannot add entries of different length')
else:
length = len(v)
length = max(1,length)
c = [{} for _ in range(length)] if constituents is None else \
[{'constituents':u} for u in ConfigMaterial._constituents(**constituents)]
if len(c) == 1: c = [c[0] for _ in range(length)]
if length != 1 and length != len(c):
raise ValueError('Cannot add entries of different length')
N,n,shaped = 1,1,{}
for k,v in kwargs.items():
if hasattr(v,'__len__') and not isinstance(v,str):
for i,vv in enumerate(v):
c[i][k] = vv.item() if isinstance(vv,np.generic) else vv
shaped[k] = np.array(v)
s = shaped[k].shape[:-1] if k=='O' else shaped[k].shape
N = max(N,s[0]) if len(s)>0 else N
n = max(n,s[1]) if len(s)>1 else n
mat = [{'constituents':[{} for _ in range(n)]} for _ in range(N)]
if 'v' not in kwargs:
shaped['v'] = np.broadcast_to(1/n,(N,n))
for k,v in shaped.items():
target = (N,n,4) if k=='O' else (N,n)
obj = np.broadcast_to(v.reshape(util.shapeshifter(v.shape,target,mode='right')),target)
for i in range(N):
if k in ['phase','O','v']:
for j in range(n):
mat[i]['constituents'][j][k] = obj[i,j].item() if isinstance(obj[i,j],np.generic) else obj[i,j]
else:
for i in range(len(c)):
c[i][k] = v
mat[i][k] = obj[i,0].item() if isinstance(obj[i,0],np.generic) else obj[i,0]
dup = self.copy()
dup['material'] = dup['material'] + c if 'material' in dup else c
dup['material'] = dup['material'] + mat if 'material' in dup else mat
return dup
@staticmethod
def _constituents(N=1,**kwargs):
"""Construct list of constituents."""
N_material=1
for v in kwargs.values():
if hasattr(v,'__len__') and not isinstance(v,str): N_material = len(v)
if N == 1:
m = [[{'v':1.0}] for _ in range(N_material)]
for k,v in kwargs.items():
if hasattr(v,'__len__') and not isinstance(v,str):
if len(v) != N_material:
raise ValueError('Cannot add entries of different length')
for i,vv in enumerate(np.array(v)):
m[i][0][k] = vv.item() if isinstance(vv,np.generic) else vv
else:
for i in range(N_material):
m[i][0][k] = v
return m
else:
raise NotImplementedError

10
python/damask/_grid.py
View File

@ -122,7 +122,7 @@ class Grid:
@size.setter
def size(self,size):
if len(size) != 3 or any(np.array(size) <= 0):
if len(size) != 3 or any(np.array(size) < 0):
raise ValueError(f'invalid size {size}')
else:
self._size = np.array(size)
@ -202,7 +202,7 @@ class Grid:
Geometry file to read.
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
try:
f = open(fname)
except TypeError:
@ -303,7 +303,7 @@ class Grid:
Need to be ordered (1./x fast, 3./z slow).
labels : str or list of str
Label(s) of the columns containing the material definition.
Each unique combintation of values results in one material ID.
Each unique combination of values results in one material ID.
"""
cells,size,origin = grid_filters.cellsSizeOrigin_coordinates0_point(table.get(coordinates))
@ -541,7 +541,7 @@ class Grid:
Compress geometry with 'x of y' and 'a to b'.
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
header = [f'{len(self.comments)+4} header'] + self.comments \
+ ['grid a {} b {} c {}'.format(*self.cells),
'size x {} y {} z {}'.format(*self.size),
@ -760,7 +760,7 @@ class Grid:
"""
if fill is None: fill = np.nanmax(self.material) + 1
dtype = float if np.isnan(fill) or int(fill) != fill or self.material.dtype==np.float else int
dtype = float if isinstance(fill,float) or self.material.dtype in np.sctypes['float'] else int
material = self.material
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')

11
python/damask/_rotation.py
View File

@ -125,9 +125,18 @@ class Rotation:
return np.logical_not(self==other)
def __array__(self):
"""Initializer for numpy."""
return self.quaternion
@property
def size(self):
return self.quaternion[...,0].size
@property
def shape(self):
return self.quaternion.shape[:-1]
return self.quaternion[...,0].shape
def __len__(self):

4
python/damask/_vtk.py
View File

@ -246,8 +246,8 @@ class VTK:
raise ValueError('No label defined for numpy.ndarray')
N_data = data.shape[0]
d = np_to_vtk((data.astype(np.float32) if data.dtype in [np.float64, np.float128]
else data).reshape(N_data,-1),deep=True) # avoid large files
d = np_to_vtk((data.astype(np.single) if data.dtype in [np.double, np.longdouble] else
data).reshape(N_data,-1),deep=True) # avoid large files
d.SetName(label)
if N_data == N_points:

2
python/damask/util.py
View File

@ -183,7 +183,7 @@ def scale_to_coprime(v):
# Python 3.9 provides math.lcm, see https://stackoverflow.com/questions/51716916.
return a * b // np.gcd(a, b)
m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(np.int)
m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
m = m//reduce(np.gcd,m)
with np.errstate(invalid='ignore'):

35
python/setup.py
View File

@ -6,28 +6,29 @@ with open(Path(__file__).parent/'damask/VERSION') as f:
version = re.sub(r'(-([^-]*)).*$',r'.\2',re.sub(r'^v(\d+\.\d+(\.\d+)?)',r'\1',f.readline().strip()))
setuptools.setup(
name="damask",
name='damask',
version=version,
author="The DAMASK team",
author_email="damask@mpie.de",
description="DAMASK library",
long_description="Python library for pre and post processing of DAMASK simulations",
url="https://damask.mpie.de",
author='The DAMASK team',
author_email='damask@mpie.de',
description='DAMASK library',
long_description='Python library for pre and post processing of DAMASK simulations',
url='https://damask.mpie.de',
packages=setuptools.find_packages(),
include_package_data=True,
python_requires = '>=3.6',
install_requires = [
"pandas", # requires numpy
"scipy",
"h5py", # requires numpy
"vtk",
"matplotlib", # requires numpy, pillow
"pyaml"
'pandas>=0.24', # requires numpy
'scipy>=1.2',
'h5py>=2.9', # requires numpy
'vtk>=8.1',
'matplotlib>=3.0', # requires numpy, pillow
'pyaml>=3.12'
],
classifiers = [
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering",
"Programming Language :: Python :: 3",
"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
"Operating System :: OS Independent",
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering',
'Programming Language :: Python :: 3',
'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
'Operating System :: OS Independent',
],
)

56
python/tests/test_ConfigMaterial.py
View File

@ -5,6 +5,7 @@ import numpy as np
from damask import ConfigMaterial
from damask import Table
from damask import Rotation
@pytest.fixture
def ref_path(ref_path_base):
@ -85,42 +86,25 @@ class TestConfigMaterial:
def test_from_table(self):
N = np.random.randint(3,10)
a = np.vstack((np.hstack((np.arange(N),np.arange(N)[::-1])),np.ones(N*2),np.zeros(N*2),np.ones(N*2))).T
t = Table(a,{'varying':2,'constant':2})
c = ConfigMaterial.from_table(t,constituents={'a':'varying','b':'1_constant'},c='2_constant')
a = np.vstack((np.hstack((np.arange(N),np.arange(N)[::-1])),np.ones(N*2),np.zeros(N*2),np.ones(N*2),np.ones(N*2))).T
t = Table(a,{'varying':1,'constant':4})
c = ConfigMaterial.from_table(t,**{'phase':'varying','O':'constant','homogenization':'4_constant'})
assert len(c['material']) == N
for i,m in enumerate(c['material']):
c = m['constituents'][0]
assert m['c'] == 1 and c['b'] == 0 and (c['a'] == [i,1]).all()
assert m['homogenization'] == 1 and (m['constituents'][0]['O'] == [1,0,1,1]).all()
def test_constituents(self):
c = ConfigMaterial._constituents(c=1,v=[2,3])
assert c[0][0]['c'] == c[1][0]['c'] == 1
assert c[0][0]['v'] == c[1][0]['v'] -1 ==2
@pytest.mark.parametrize('constituents',[{'W':1,'X':[2,3]},{'Y':4},{'Z':[5,6]}])
@pytest.mark.parametrize('a',[[7.,8.],9.])
@pytest.mark.parametrize('b',['bd',['efg','hi']])
def test_material_add(self,tmp_path,constituents,a,b):
len_c = len(ConfigMaterial()._constituents(1,**constituents))
len_a = len(a) if isinstance(a,list) else 1
len_b = len(b) if isinstance(b,list) else 1
m = ConfigMaterial().material_add(constituents,a=a,b=b)
m.save()
assert len(m['material']) == np.max([len_a,len_b,len_c])
@pytest.mark.parametrize('constituents',[{'W':1,'X':np.array([2,3])},{'Y':4},{'Z':np.array([5,6])}])
@pytest.mark.parametrize('a',[np.array([7,8]),9])
def test_material_add_np(self,tmp_path,constituents,a):
len_c = len(ConfigMaterial()._constituents(1,**constituents))
len_a = len(a) if isinstance(a,np.ndarray) else 1
m = ConfigMaterial().material_add(constituents,ld=a)
m.save()
assert len(m['material']) == np.max([len_a,len_c])
@pytest.mark.parametrize('constituents',[{'X':np.array([2,3,4,5])},{'Y':4}])
@pytest.mark.parametrize('a',[np.array([1,2,3]),[4,5,6]])
@pytest.mark.parametrize('b',[np.array([6.,7.]),[8.,9.]])
def test_material_add_invalid(self,constituents,a,b):
with pytest.raises(ValueError):
ConfigMaterial().material_add(constituents,a=a,u=b)
@pytest.mark.parametrize('N,n,kw',[
(1,1,{'phase':'Gold',
'O':[1,0,0,0],
'homogenization':'SX'}),
(3,1,{'phase':'Gold',
'O':Rotation.from_random(3),
'homogenization':'SX'}),
(2,3,{'phase':np.broadcast_to(['a','b','c'],(2,3)),
'O':Rotation.from_random((2,3)),
'homogenization':['SX','PX']}),
])
def test_material_add(self,kw,N,n):
m = ConfigMaterial().material_add(**kw)
assert len(m['material']) == N
assert len(m['material'][0]['constituents']) == n

2
python/tests/test_Grid.py
View File

@ -347,7 +347,7 @@ class TestGrid:
@pytest.mark.parametrize('approach',['Laguerre','Voronoi'])
def test_tessellate_bicrystal(self,approach):
cells = np.random.randint(5,10,3)*2
size = cells.astype(np.float)
size = cells.astype(float)
seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
material = np.zeros(cells)
material[:,cells[1]//2:,:] = 1

10
python/tests/test_Rotation.py
View File

@ -689,6 +689,10 @@ class TestRotation:
with pytest.raises(TypeError):
Rotation(np.ones(3))
def test_to_numpy(self):
r = Rotation.from_random(np.random.randint(0,10,4))
assert np.all(r.as_quaternion() == np.array(r))
@pytest.mark.parametrize('degrees',[True,False])
def test_Eulers(self,set_of_rotations,degrees):
for rot in set_of_rotations:
@ -804,7 +808,11 @@ class TestRotation:
r = Rotation.from_random()
assert r == ~~r
@pytest.mark.parametrize('shape',[None,1,(1,),(4,2),(1,1,1)])
@pytest.mark.parametrize('shape',[1,(1,),(4,2),(1,1,1),tuple(np.random.randint(0,10,4))])
def test_size(self,shape):
assert Rotation.from_random(shape).size == np.prod(shape)
@pytest.mark.parametrize('shape',[None,1,(1,),(4,2),(1,1,1),tuple(np.random.randint(0,10,4))])
def test_shape(self,shape):
r = Rotation.from_random(shape=shape)
assert r.shape == (shape if isinstance(shape,tuple) else (shape,) if shape else ())

9
src/CPFEM2.f90
View File

@ -75,7 +75,6 @@ end subroutine CPFEM_initAll
subroutine CPFEM_init
integer(HID_T) :: fileHandle
character(len=pStringLen) :: fileName
print'(/,a)', ' <<<+- CPFEM init -+>>>'; flush(IO_STDOUT)
@ -83,8 +82,8 @@ subroutine CPFEM_init
if (interface_restartInc > 0) then
print'(/,a,i0,a)', ' reading restart information of increment from file'; flush(IO_STDOUT)
write(fileName,'(a,i0,a)') trim(getSolverJobName())//'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName)
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','r')
call homogenization_restartRead(fileHandle)
call phase_restartRead(fileHandle)
@ -101,13 +100,11 @@ end subroutine CPFEM_init
subroutine CPFEM_restartWrite
integer(HID_T) :: fileHandle
character(len=pStringLen) :: fileName
print*, ' writing field and constitutive data required for restart to file';flush(IO_STDOUT)
write(fileName,'(a,i0,a)') trim(getSolverJobName())//'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName,'a')
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','a')
call homogenization_restartWrite(fileHandle)
call phase_restartWrite(fileHandle)

68
src/HDF5_utilities.f90
View File

@ -71,6 +71,12 @@ module HDF5_utilities
module procedure HDF5_addAttribute_real_array
end interface HDF5_addAttribute
#ifdef PETSc
logical, parameter, private :: parallel_default = .true.
#else
logical, parameter, private :: parallel_default = .false.
#endif
contains
@ -105,16 +111,16 @@ end subroutine HDF5_utilities_init
!--------------------------------------------------------------------------------------------------
!> @brief open and initializes HDF5 output file
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_openFile(fileName,mode,parallel)
integer(HID_T) function HDF5_openFile(fileName,mode)
character(len=*), intent(in) :: fileName
character, intent(in), optional :: mode
logical, intent(in), optional :: parallel
character :: m
integer(HID_T) :: plist_id
integer :: hdferr
if (present(mode)) then
m = mode
else
@ -125,10 +131,8 @@ integer(HID_T) function HDF5_openFile(fileName,mode,parallel)
if(hdferr < 0) error stop 'HDF5 error'
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
endif; endif
#endif
if (m == 'w') then
@ -547,7 +551,7 @@ subroutine HDF5_read_real1(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -587,7 +591,7 @@ subroutine HDF5_read_real2(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -627,7 +631,7 @@ subroutine HDF5_read_real3(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -667,7 +671,7 @@ subroutine HDF5_read_real4(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -707,7 +711,7 @@ subroutine HDF5_read_real5(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -747,7 +751,7 @@ subroutine HDF5_read_real6(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -787,7 +791,7 @@ subroutine HDF5_read_real7(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -829,7 +833,7 @@ subroutine HDF5_read_int1(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -869,7 +873,7 @@ subroutine HDF5_read_int2(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -909,7 +913,7 @@ subroutine HDF5_read_int3(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -949,7 +953,7 @@ subroutine HDF5_read_int4(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -989,7 +993,7 @@ subroutine HDF5_read_int5(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -1029,7 +1033,7 @@ subroutine HDF5_read_int6(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -1069,7 +1073,7 @@ subroutine HDF5_read_int7(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -1109,7 +1113,7 @@ subroutine HDF5_write_real1(loc_id,dataset,datasetName,parallel)
myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1150,7 +1154,7 @@ subroutine HDF5_write_real2(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1191,7 +1195,7 @@ subroutine HDF5_write_real3(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1232,7 +1236,7 @@ subroutine HDF5_write_real4(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1274,7 +1278,7 @@ subroutine HDF5_write_real5(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1315,7 +1319,7 @@ subroutine HDF5_write_real6(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1356,7 +1360,7 @@ subroutine HDF5_write_real7(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1398,7 +1402,7 @@ subroutine HDF5_write_int1(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1439,7 +1443,7 @@ subroutine HDF5_write_int2(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1480,7 +1484,7 @@ subroutine HDF5_write_int3(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1521,7 +1525,7 @@ subroutine HDF5_write_int4(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1562,7 +1566,7 @@ subroutine HDF5_write_int5(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1603,7 +1607,7 @@ subroutine HDF5_write_int6(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1644,7 +1648,7 @@ subroutine HDF5_write_int7(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then

2
src/grid/DAMASK_grid.f90
View File

@ -225,8 +225,8 @@ program DAMASK_grid
loadCases(l)%t = step_discretization%get_asFloat('t')
loadCases(l)%N = step_discretization%get_asInt ('N')
loadCases(l)%r = step_discretization%get_asFloat('r', defaultVal= 1.0_pReal)
loadCases(l)%f_restart = step_discretization%get_asInt ('f_restart', defaultVal=huge(0))
loadCases(l)%f_restart = load_step%get_asInt('f_restart', defaultVal=huge(0))
loadCases(l)%f_out = load_step%get_asInt('f_out', defaultVal=1)
loadCases(l)%estimate_rate = (load_step%get_asBool('estimate_rate',defaultVal=.true.) .and. &
merge(.true.,.false.,l > 1))

7
src/grid/discretization_grid.f90
View File

@ -68,8 +68,11 @@ subroutine discretization_grid_init(restart)
print'(/,a)', ' <<<+- discretization_grid init -+>>>'; flush(IO_STDOUT)
if(worldrank == 0) call readVTR(grid,geomSize,origin,materialAt_global)
if(worldrank == 0) then
call readVTR(grid,geomSize,origin,materialAt_global)
else
allocate(materialAt_global(0)) ! needed for IntelMPI
endif
call MPI_Bcast(grid,3,MPI_INTEGER,0,PETSC_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'

10
src/grid/grid_mech_FEM.f90
View File

@ -108,8 +108,6 @@ subroutine grid_mechanical_FEM_init
u_current,u_lastInc
PetscInt, dimension(0:worldsize-1) :: localK
integer(HID_T) :: fileHandle, groupHandle
character(len=pStringLen) :: &
fileName
class(tNode), pointer :: &
num_grid, &
debug_grid
@ -234,8 +232,7 @@ subroutine grid_mechanical_FEM_init
restartRead: if (interface_restartInc > 0) then
print'(/,a,i0,a)', ' reading restart data of increment ', interface_restartInc, ' from file'
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName)
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','r')
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_read(groupHandle,P_aim, 'P_aim')
@ -422,7 +419,7 @@ subroutine grid_mechanical_FEM_restartWrite
PetscErrorCode :: ierr
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: u_current,u_lastInc
character(len=pStringLen) :: fileName
call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,ierr)
CHKERRQ(ierr)
@ -431,8 +428,7 @@ subroutine grid_mechanical_FEM_restartWrite
print*, 'writing solver data required for restart to file'; flush(IO_STDOUT)
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName,'w')
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
groupHandle = HDF5_addGroup(fileHandle,'solver')
call HDF5_write(groupHandle,P_aim, 'P_aim')

9
src/grid/grid_mech_spectral_basic.f90
View File

@ -99,8 +99,6 @@ subroutine grid_mechanical_spectral_basic_init
PetscInt, dimension(0:worldsize-1) :: localK
integer(HID_T) :: fileHandle, groupHandle
integer :: fileUnit
character(len=pStringLen) :: &
fileName
class (tNode), pointer :: &
num_grid, &
debug_grid
@ -182,8 +180,7 @@ subroutine grid_mechanical_spectral_basic_init
restartRead: if (interface_restartInc > 0) then
print'(/,a,i0,a)', ' reading restart data of increment ', interface_restartInc, ' from file'
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName)
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','r')
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_read(groupHandle,P_aim, 'P_aim')
@ -365,14 +362,12 @@ subroutine grid_mechanical_spectral_basic_restartWrite
PetscErrorCode :: ierr
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: F
character(len=pStringLen) :: fileName
call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
print*, 'writing solver data required for restart to file'; flush(IO_STDOUT)
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName,'w')
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
groupHandle = HDF5_addGroup(fileHandle,'solver')
call HDF5_write(groupHandle,P_aim, 'P_aim')

9
src/grid/grid_mech_spectral_polarisation.f90
View File

@ -112,8 +112,6 @@ subroutine grid_mechanical_spectral_polarisation_init
PetscInt, dimension(0:worldsize-1) :: localK
integer(HID_T) :: fileHandle, groupHandle
integer :: fileUnit
character(len=pStringLen) :: &
fileName
class (tNode), pointer :: &
num_grid, &
debug_grid
@ -204,8 +202,7 @@ subroutine grid_mechanical_spectral_polarisation_init
restartRead: if (interface_restartInc > 0) then
print'(/,a,i0,a)', ' reading restart data of increment ', interface_restartInc, ' from file'
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName)
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','r')
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_read(groupHandle,P_aim, 'P_aim')
@ -419,7 +416,6 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
PetscErrorCode :: ierr
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: FandF_tau, F, F_tau
character(len=pStringLen) :: fileName
call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
F => FandF_tau(0: 8,:,:,:)
@ -427,8 +423,7 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
print*, 'writing solver data required for restart to file'; flush(IO_STDOUT)
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName,'w')
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
groupHandle = HDF5_addGroup(fileHandle,'solver')
call HDF5_write(groupHandle,F_aim, 'P_aim')

41
src/results.f90
View File

@ -65,7 +65,7 @@ subroutine results_init(restart)
print*, 'https://doi.org/10.1007/s40192-017-0084-5'//IO_EOL
if(.not. restart) then
resultsFile = HDF5_openFile(trim(getSolverJobName())//'.hdf5','w',.true.)
resultsFile = HDF5_openFile(getSolverJobName()//'.hdf5','w')
call results_addAttribute('DADF5_version_major',0)
call results_addAttribute('DADF5_version_minor',11)
call results_addAttribute('DAMASK_version',DAMASKVERSION)
@ -83,7 +83,7 @@ end subroutine results_init
!--------------------------------------------------------------------------------------------------
subroutine results_openJobFile
resultsFile = HDF5_openFile(trim(getSolverJobName())//'.hdf5','a',.true.)
resultsFile = HDF5_openFile(getSolverJobName()//'.hdf5','a')
end subroutine results_openJobFile
@ -289,11 +289,7 @@ subroutine results_writeScalarDataset_real(group,dataset,label,description,SIuni
groupHandle = results_openGroup(group)
#ifdef PETSc
call HDF5_write(groupHandle,dataset,label,.true.)
#else
call HDF5_write(groupHandle,dataset,label,.false.)
#endif
call HDF5_write(groupHandle,dataset,label)
if (HDF5_objectExists(groupHandle,label)) &
call HDF5_addAttribute(groupHandle,'Description',description,label)
@ -320,11 +316,7 @@ subroutine results_writeVectorDataset_real(group,dataset,label,description,SIuni
groupHandle = results_openGroup(group)
#ifdef PETSc
call HDF5_write(groupHandle,dataset,label,.true.)
#else
call HDF5_write(groupHandle,dataset,label,.false.)
#endif
call HDF5_write(groupHandle,dataset,label)
if (HDF5_objectExists(groupHandle,label)) &
call HDF5_addAttribute(groupHandle,'Description',description,label)
@ -362,7 +354,7 @@ subroutine results_writeTensorDataset_real(group,dataset,label,description,SIuni
endif
if(transposed_) then
if(size(dataset,1) /= size(dataset,2)) call IO_error(0,ext_msg='transpose non-symmetric tensor')
if(size(dataset,1) /= size(dataset,2)) error stop 'transpose non-symmetric tensor'
allocate(dataset_transposed,mold=dataset)
do i=1,size(dataset_transposed,3)
dataset_transposed(:,:,i) = transpose(dataset(:,:,i))
@ -373,11 +365,7 @@ subroutine results_writeTensorDataset_real(group,dataset,label,description,SIuni
groupHandle = results_openGroup(group)
#ifdef PETSc
call HDF5_write(groupHandle,dataset_transposed,label,.true.)
#else
call HDF5_write(groupHandle,dataset_transposed,label,.false.)
#endif
call HDF5_write(groupHandle,dataset_transposed,label)
if (HDF5_objectExists(groupHandle,label)) &
call HDF5_addAttribute(groupHandle,'Description',description,label)
@ -405,11 +393,7 @@ subroutine results_writeVectorDataset_int(group,dataset,label,description,SIunit
groupHandle = results_openGroup(group)
#ifdef PETSc
call HDF5_write(groupHandle,dataset,label,.true.)
#else
call HDF5_write(groupHandle,dataset,label,.false.)
#endif
call HDF5_write(groupHandle,dataset,label)
if (HDF5_objectExists(groupHandle,label)) &
call HDF5_addAttribute(groupHandle,'Description',description,label)
@ -437,11 +421,7 @@ subroutine results_writeTensorDataset_int(group,dataset,label,description,SIunit
groupHandle = results_openGroup(group)
#ifdef PETSc
call HDF5_write(groupHandle,dataset,label,.true.)
#else
call HDF5_write(groupHandle,dataset,label,.false.)
#endif
call HDF5_write(groupHandle,dataset,label)
if (HDF5_objectExists(groupHandle,label)) &
call HDF5_addAttribute(groupHandle,'Description',description,label)
@ -577,7 +557,7 @@ subroutine results_mapping_phase(phaseAt,memberAtLocal,label)
!--------------------------------------------------------------------------------------------------
! write the components of the compound type individually
call h5pset_preserve_f(plist_id, .TRUE., hdferr)
call h5pset_preserve_f(plist_id, .true., hdferr)
if(hdferr < 0) error stop 'HDF5 error'
loc_id = results_openGroup('/mapping')
@ -733,7 +713,8 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
!--------------------------------------------------------------------------------------------------
! write the components of the compound type individually
call h5pset_preserve_f(plist_id, .TRUE., hdferr)
call h5pset_preserve_f(plist_id, .true., hdferr)
if(hdferr < 0) error stop 'HDF5 error'
loc_id = results_openGroup('/mapping')
call h5dcreate_f(loc_id, 'homogenization', dtype_id, filespace_id, dset_id, hdferr)