error 844 #67

Propionates · 2025-04-18T06:14:32Z

Propionates
Apr 18, 2025

Hello, could anybody help me? I tried to run a simulation, but this error occurred. It says invalid size of the VTI file like this and when I tried to cut the EBSD data it still error. Thank you

Here I attached the geom file
ebsd_vti.txt

DAMASK_grid -g ebsd.vti -m SUS316L_material.yaml -l tensionX.yaml

 <<<+-  parallelization init  -+>>>

 Open MPI v4.1.6, package: Debian OpenMPI, ident: 4.1.6, repo rev: v4.1.6, Sep 30, 2023
 MPI standard: 3.1
 OpenMP version: 201511

 MPI processes: 1
 Could not get $OMP_NUM_THREADS, using default
 OMP_NUM_THREADS: 4

 <<<+-  CLI init  -+>>>

     _/_/_/      _/_/    _/      _/    _/_/      _/_/_/  _/    _/    _/_/_/
    _/    _/  _/    _/  _/_/  _/_/  _/    _/  _/        _/  _/            _/
   _/    _/  _/_/_/_/  _/  _/  _/  _/_/_/_/    _/_/    _/_/          _/_/
  _/    _/  _/    _/  _/      _/  _/    _/        _/  _/  _/            _/
 _/_/_/    _/    _/  _/      _/  _/    _/  _/_/_/    _/    _/    _/_/_/
 Grid solver

 F. Roters et al., Computational Materials Science 158:420–478, 2019
 https://doi.org/10.1016/j.commatsci.2018.04.030

 S. Balay et al., PETSc/TAO User Manual Revision 3.19
 https://doi.org/10.2172/1968587

 Version: v3.0.1

 Compiled with: GCC version 13.3.0
 Compiled on: Linux-6.8.0-51-generic
 Compiler options: -cpp -I /usr/lib/petscdir/petsc3.19/x86_64-linux-gnu-real/include -I /usr/include/hypre -I /usr/include/suitesparse -I /usr/include/superlu -I /usr/include/superlu-dist -I /usr/include/trilinos -I /usr/include/scotch -I /usr/include/hdf5/openmpi -I /usr/include/hdf5/serial -I /usr/include -I /usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi -I /usr/lib/x86_64-linux-gnu/openmpi/lib -imultiarch x86_64-linux-gnu -D_REENTRANT -D CMAKE_SYSTEM="Linux-6.8.0-51-generic" -D DAMASKVERSION="v3.0.1" -D FYAML -D GRID -D PETSC --param=l1-cache-size=32 --param=l1-cache-line-size=64 --param=l2-cache-size=512 -mtune=znver2 -mno-omit-leaf-frame-pointer -march=x86-64 -g -O2 -O2 -Wall -Wextra -Wcharacter-truncation -Wunderflow -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wconversion-extra -Wunused-parameter -std=f2018 -fno-omit-frame-pointer -ffile-prefix-map=/build/damask-XEckOy/damask-3.0.1=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fdebug-prefix-map=/build/damask-XEckOy/damask-3.0.1=/usr/src/damask-3.0.1-6~noble -fopenmp -fPIE -ffree-line-length-none -fimplicit-none -fallow-argument-mismatch -ffpe-summary=all -fpre-include=/usr/include/finclude/x86_64-linux-gnu/math-vector-fortran.h

 Compiled on: Jan 14 2025 at 07:40:31

 PETSc version: 3.19.6

 Date: 18/04/2025
 Time: 15:03:11

 Host name: DESKTOP-GDK0V69
 User name: jesica

 Command line call:      DAMASK_grid -g ebsd.vti -m SUS316L_material.yaml -l tensionX.yaml

 Working directory:      /mnt/h/kuliah/TA/damask/pre-processing
 Geometry:               ebsd.vti
 Load case:              tensionX.yaml
 Material config:        SUS316L_material.yaml
 Solver job name:        ebsd_tensionX_SUS316L_material

 <<<+-  system_routines init  -+>>>

 <<<+-  prec init  -+>>>

 integer size / bit:   32
   maximum value:              2147483647

 real size / bit:      64
   maximum value:      0.180+309
   minimum value:      0.223-307
   epsilon value:      0.222E-15
   decimal precision:  15

 <<<+-  misc init  -+>>>

 <<<+-  IO init  -+>>>

 <<<+-  base64 init  -+>>>

 <<<+-  types init  -+>>>

 <<<+-  YAML init  -+>>>

 libfyaml powered

 <<<+-  HDF5_utilities init  -+>>>

 <<<+-  result init  -+>>>

 M. Diehl et al., Integrating Materials and Manufacturing Innovation 6(1):83–91, 2017
 https://doi.org/10.1007/s40192-017-0084-5

 <<<+-  config init  -+>>>

 reading material configuration

 <<<+-  math init  -+>>>

 size  of random seed:      8
 value of random seed:       -577520204  -187758254  2128522822   691732539   578615677   -20104578  1178059655   894721043
 start of random sequence:
                           0.51335955782465
                           0.07413682569116
                           0.51821199840101
                           0.13739707772188

 <<<+-  rotations init  -+>>>

 D. Rowenhorst et al., Modelling and Simulation in Materials Science and Engineering 23:083501, 2015
 https://doi.org/10.1088/0965-0393/23/8/083501

 <<<+-  polynomials init  -+>>>

 <<<+-  tables init  -+>>>

 <<<+-  crystal init  -+>>>

 <<<+-  discretization_grid init  -+>>>

 ┌─────────────────────────────────────────────────────────────────────┐
 │                        error 844                                    │
 ├─────────────────────────────────────────────────────────────────────┤
 │ invalid VTI file                                                    │
 │ size                                                                │
 │                                                                     │
 └─────────────────────────────────────────────────────────────────────┘

 DAMASK terminated on:
 Date:               18/04/2025
 Time:               15:03:12
Note: The following floating-point exceptions are signalling: IEEE_INEXACT_FLAG
STOP 1

Answered by eisenlohr

Apr 18, 2025

This error indicates that (at least) one of the grid sizes is non-positive.
For the file you provided, which is a 2D map, the third dimension has zero thickness:

>>> import numpy as np
>>> import damask
>>> grid=damask.GeomGrid.load('ebsd.vti')
>>> grid
cells:  56 × 48 × 1
size:   55.99999999999999 × 47.99999999999999 × 0.0 m³
origin: -55.5   -0.49999999999999994   0.0 m
# materials: 2669

Set the thickness to, for instance, the smaller cell dimension along the other two directions:

>>> grid.size[2] = grid.cells[2]*np.min((grid.size/grid.cells)[:2])
>>> grid
cells:  56 × 48 × 1
size:   55.99999999999999 × 47.99999999999999 × 0.9999999999999999 m³
origin: -55.5   -0.49999999999999994   0.0 m
…

View full answer

eisenlohr · 2025-04-18T13:41:10Z

eisenlohr
Apr 18, 2025
Maintainer

This error indicates that (at least) one of the grid sizes is non-positive.
For the file you provided, which is a 2D map, the third dimension has zero thickness:

>>> import numpy as np
>>> import damask
>>> grid=damask.GeomGrid.load('ebsd.vti')
>>> grid
cells:  56 × 48 × 1
size:   55.99999999999999 × 47.99999999999999 × 0.0 m³
origin: -55.5   -0.49999999999999994   0.0 m
# materials: 2669

Set the thickness to, for instance, the smaller cell dimension along the other two directions:

>>> grid.size[2] = grid.cells[2]*np.min((grid.size/grid.cells)[:2])
>>> grid
cells:  56 × 48 × 1
size:   55.99999999999999 × 47.99999999999999 × 0.9999999999999999 m³
origin: -55.5   -0.49999999999999994   0.0 m
# materials: 2669

DAMASK versions after 3.0.1 will have more informative messages regarding VTI parsing errors.

3 replies

Propionates Apr 21, 2025
Author

Thank you for your replies. It works after I change the non-positive grid sizes, but now I have encountered material error that says invalid orientation specified.
Here is my material file
SUS316L_material_yaml.txt

DAMASK_grid -g ebsd.vti -l tensionX.yaml -m SUS316L_material.yaml

 <<<+-  parallelization init  -+>>>

 Open MPI v4.1.6, package: Debian OpenMPI, ident: 4.1.6, repo rev: v4.1.6, Sep 30, 2023
 MPI standard: 3.1
 OpenMP version: 201511

 MPI processes: 1
 Could not get $OMP_NUM_THREADS, using default
 OMP_NUM_THREADS: 4

 <<<+-  CLI init  -+>>>

     _/_/_/      _/_/    _/      _/    _/_/      _/_/_/  _/    _/    _/_/_/
    _/    _/  _/    _/  _/_/  _/_/  _/    _/  _/        _/  _/            _/
   _/    _/  _/_/_/_/  _/  _/  _/  _/_/_/_/    _/_/    _/_/          _/_/
  _/    _/  _/    _/  _/      _/  _/    _/        _/  _/  _/            _/
 _/_/_/    _/    _/  _/      _/  _/    _/  _/_/_/    _/    _/    _/_/_/
 Grid solver

 F. Roters et al., Computational Materials Science 158:420–478, 2019
 https://doi.org/10.1016/j.commatsci.2018.04.030

 S. Balay et al., PETSc/TAO User Manual Revision 3.19
 https://doi.org/10.2172/1968587

 Version: v3.0.1

 Compiled with: GCC version 13.3.0
 Compiled on: Linux-6.8.0-51-generic
 Compiler options: -cpp -I /usr/lib/petscdir/petsc3.19/x86_64-linux-gnu-real/include -I /usr/include/hypre -I /usr/include/suitesparse -I /usr/include/superlu -I /usr/include/superlu-dist -I /usr/include/trilinos -I /usr/include/scotch -I /usr/include/hdf5/openmpi -I /usr/include/hdf5/serial -I /usr/include -I /usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi -I /usr/lib/x86_64-linux-gnu/openmpi/lib -imultiarch x86_64-linux-gnu -D_REENTRANT -D CMAKE_SYSTEM="Linux-6.8.0-51-generic" -D DAMASKVERSION="v3.0.1" -D FYAML -D GRID -D PETSC --param=l1-cache-size=32 --param=l1-cache-line-size=64 --param=l2-cache-size=512 -mtune=znver2 -mno-omit-leaf-frame-pointer -march=x86-64 -g -O2 -O2 -Wall -Wextra -Wcharacter-truncation -Wunderflow -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wconversion-extra -Wunused-parameter -std=f2018 -fno-omit-frame-pointer -ffile-prefix-map=/build/damask-XEckOy/damask-3.0.1=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fdebug-prefix-map=/build/damask-XEckOy/damask-3.0.1=/usr/src/damask-3.0.1-6~noble -fopenmp -fPIE -ffree-line-length-none -fimplicit-none -fallow-argument-mismatch -ffpe-summary=all -fpre-include=/usr/include/finclude/x86_64-linux-gnu/math-vector-fortran.h

 Compiled on: Jan 14 2025 at 07:40:31

 PETSc version: 3.19.6

 Date: 21/04/2025
 Time: 14:35:18

 Host name: DESKTOP-GDK0V69
 User name: jesica

 Command line call:      DAMASK_grid -g ebsd.vti -l tensionX.yaml -m SUS316L_material.yaml

 Working directory:      /mnt/h/kuliah/TA/damask/pre-processing
 Geometry:               ebsd.vti
 Load case:              tensionX.yaml
 Material config:        SUS316L_material.yaml
 Solver job name:        ebsd_tensionX_SUS316L_material

 <<<+-  system_routines init  -+>>>

 <<<+-  prec init  -+>>>

 integer size / bit:   32
   maximum value:              2147483647

 real size / bit:      64
   maximum value:      0.180+309
   minimum value:      0.223-307
   epsilon value:      0.222E-15
   decimal precision:  15

 <<<+-  misc init  -+>>>

 <<<+-  IO init  -+>>>

 <<<+-  base64 init  -+>>>

 <<<+-  types init  -+>>>

 <<<+-  YAML init  -+>>>

 libfyaml powered

 <<<+-  HDF5_utilities init  -+>>>

 <<<+-  result init  -+>>>

 M. Diehl et al., Integrating Materials and Manufacturing Innovation 6(1):83–91, 2017
 https://doi.org/10.1007/s40192-017-0084-5

 <<<+-  config init  -+>>>

 reading material configuration

 <<<+-  math init  -+>>>

 size  of random seed:      8
 value of random seed:       1469056750 -1115216069   557865938  1428924092  -151569045  -432855532  1786090823  1234471945
 start of random sequence:
                           0.30329353421521
                           0.32073501725841
                           0.98985103940922
                           0.99938355677935

 <<<+-  rotations init  -+>>>

 D. Rowenhorst et al., Modelling and Simulation in Materials Science and Engineering 23:083501, 2015
 https://doi.org/10.1088/0965-0393/23/8/083501

 <<<+-  polynomials init  -+>>>

 <<<+-  tables init  -+>>>

 <<<+-  crystal init  -+>>>

 <<<+-  discretization_grid init  -+>>>

 cells:  56 × 48 × 1
 size:   5.60E+01 × 4.80E+01 × 1.00E+00 m³
 origin: -5.55E+01 -5.00E-01  0.00E+00 m

 <<<+-  discretization init  -+>>>

 <<<+-  material init  -+>>>

 ┌─────────────────────────────────────────────────────────────────────┐
 │                        error 402                                    │
 ├─────────────────────────────────────────────────────────────────────┤
 │ invalid orientation specified                                       │
 │ fromQuaternion                                                      │
 │                                                                     │
 └─────────────────────────────────────────────────────────────────────┘

 DAMASK terminated on:
 Date:               21/04/2025
 Time:               14:35:18
Note: The following floating-point exceptions are signalling: IEEE_INEXACT_FLAG
STOP 1

eisenlohr Apr 21, 2025
Maintainer

The SUS316L_material.yaml file contains orientation information for which the $q_0$ part is negative and the norm is too far off unity, e.g., the third entry.

Please see https://damask-multiphysics.org/documentation/processing_tools/pre-processing.html#damask.Rotation.from_quaternion for allowable values of quaternion specifications.

My suggestion is to use damask.Rotation.from_quaternion to check the validity of all your quaternion data in SUS316L_material.yaml. You will find multiple problems regarding negative $q_0$ as well as limited precision such that the resulting quaternion norm is not close enough to unity ($|\mathbf{q}| \ne 1$).

Both problems can be fixed by reading the quaternion data from SUS316L_material.yaml with damask.Rotation.from_quaternion() using accept_homomorph=True and normalize=True, then re-exporting the adjusted values...

Propionates Apr 22, 2025
Author

Thank you very much, now it is working

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