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pyhyp's Introduction

pyHyp

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pyHyp uses hyperbolic volume mesh marching schemes to extrude structured surface meshes into volume meshes. pyHyp is used as a preprocessing step in the geometry and mesh-creation process prior to an optimization.

Documentation

Please see the documentation for installation details and API documentation.

To locally build the documentation, enter the doc folder and enter make html in terminal. You can then view the built documentation in the _build folder.

Citation

If you use pyHyp in any publication for which you find it useful, please cite this paper.

N. Secco, G. K. W. Kenway, P. He, C. A. Mader, and J. R. R. A. Martins, “Efficient Mesh Generation and Deformation for Aerodynamic Shape Optimization”, AIAA Journal, 2021. doi:10.2514/1.J059491

@article{Secco2021,
    title = {Efficient Mesh Generation and Deformation for Aerodynamic Shape Optimization},
    author = {Ney Secco and Gaetan K. W. Kenway and Ping He and Charles A. Mader and Joaquim R. R. A. Martins},
    doi = {10.2514/1.J059491},
    journal = {AIAA Journal},
    year = {2021}
}

How pyHyp fits within MACH

pyHyp takes structured surface meshes and extrudes them into structured volume meshes. This is done as a pre-processing step. Generally, the surface meshes come from ICEM. The pyHyp-generated volume meshes are then used in ADflow to perform CFD. An example XDSM for an optimization setup that uses pyHyp is shown below.

pySurf XDSM diagram

License

Copyright 2019 MDO Lab. See the LICENSE file for details.

pyhyp's People

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pyhyp's Issues

hyp.writeCGNS fails

I've managed to install pyhyp and got the message
Testing if module hyp can be imported...
Module hyp was successfully imported.

Then I ran the example case from the python/examples/2D folder and I received the following error
Traceback (most recent call last):
File "naca0012_euler.py", line 105, in
hyp.writeCGNS('naca0012_euler.cgns')
File "/home/jethro/repos/pyhyp/python/pyHyp.py", line 747, in writeCGNS
autoconnect was NOT performed")
pyhyp.python.pyHyp.Error
*** The MPI_Attr_get() function was called after MPI_FINALIZE was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.

I do not know how to solve this problem.

Thanks for your help.

Compile Issue: writeCGNS.F90 Symbol bcfarfield has no implicit type

Hi. This might be a config error on my part, but I'm trying to build using gcc-7.2.0, cgns 4.2.0, and petsc 3.15.5 and am getting this error:

`
mpifort -I../../mod -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/cgns-4.2.0-emrmffjw7xwd5vmp347xy6tnh6bolwpg/include -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/hdf5-1.10.6-72ul7tgf72iqljxqq2wnkfxq4mvcbisn/include -fPIC -std=f2008 -fdefault-real-8 -O2 -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/petsc-3.15.5-j24jyfmmfq3hwnc7ze33ajrhoyqxzfjz/include -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/hypre-2.22.0-v5w476ssljujxrsg5w6tjac7xrgvlsp6/include -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/superlu-dist-7.2.0-lx3sqeqqt2dkfjb5jln65e3dznidilh3/include -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/cgns-4.2.0-emrmffjw7xwd5vmp347xy6tnh6bolwpg/include -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/hdf5-1.10.6-72ul7tgf72iqljxqq2wnkfxq4mvcbisn/include -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/parmetis-4.0.3-b57avbwf3yv3kmmxlejzm7kv6m3unjgs/include -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/metis-5.1.0-gp45psarg3skmytc3724dldlk6ggrn3n/include -I/usr/include -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/petsc-3.15.5-j24jyfmmfq3hwnc7ze33ajrhoyqxzfjz/include -I/usr/netpub/pyhyp/spack-manager/spack/opt/spack/linux-rhel7-x86_64/gcc-7.2.0/hdf5-1.10.6-72ul7tgf72iqljxqq2wnkfxq4mvcbisn/include -c writeLayer.F90 -o ../../obj/writeLayer.o
writeCGNS.F90:172:31:

     call writeBC(bcFarField, ptRange, "Far")
                           1

Error: Symbol 'bcfarfield' at (1) has no IMPLICIT type
writeCGNS.F90:199:39:

        call writeBC(BCSymmetryPlane, ptRange, "Sym")
                                   1

Error: Symbol 'bcsymmetryplane' at (1) has no IMPLICIT type
writeCGNS.F90:167:31:

  call writeBC(bcWallViscous, ptRange, families(iPatch))
                           1

Error: Symbol 'bcwallviscous' at (1) has no IMPLICIT type
writeCGNS.F90:119:59:

        call cg_coord_write_f(cg, base, zone, realDouble, &
                                                       1

Error: Symbol 'realdouble' at (1) has no IMPLICIT type
writeCGNS.F90:82:66:

     call cg_zone_write_f(cg, base, zonename, sizes, Structured, &
                                                              1

Error: Symbol 'structured' at (1) has no IMPLICIT type
writeCGNS.F90:127:69:

        call cg_sol_write_f(cg, base, zone, "FlowSolution", Vertex, s, ierr)
                                                                 1

Error: Symbol 'vertex' at (1) has no IMPLICIT type
writeCGNS.F90:259:30:

         BCType, PointRange, 2_cgsize_t, ptRange, BCout, ierr)
                          1

Error: Symbol 'pointrange' at (1) has no IMPLICIT type
`

Has anyway seen this before? Am I linking CGNS improperly? Any hints on how to fix?

Thanks for any help!

Failed to generate mesh

Hi ! I'm new on pyhyp and linux systems overall. I've tried some tutorial cases and they worked perfectly. But whenever I tried to generate a volume mesh with my own geometry, I got these errors:
_ with a CGNS : "VSPAERO Viewer Not Found. cgio_open_file:invalid file type"
_ with a PLOT3D: "VSPAERO Viewer Not Found. Fortran runtime error: Bad integer for item 1 in list input"
Does anyone have an idea of the origin of the bug ?

Can't compile with '-std=f2008'

Description

Basically the same as: mdolab/idwarp#70

Steps to reproduce issue

  1. Try compiling it with the default 'config.LINUX_GFORTRAN_OPENMPI.mk'

Current behavior

...
make     src_2
make[3]: Entering directory '/home/andv/Downloads/MACH/pyhyp/src/modules'
../../rulesSources.mk:43: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:43: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:31: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:31: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:37: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:37: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:31: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:31: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:37: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:37: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:25: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:25: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:19: warning: ignoring prerequisites on suffix rule definition
../../rulesSources.mk:19: warning: ignoring prerequisites on suffix rule definition
mpifort -I../../mod -I/home/andv/.mamba/envs/MACH/external/cgns/include -I/home/andv/.mamba/envs/MACH/external/hdf5/include -fPIC -std=f2008 -fdefault-real-8 -O2 -I/home/andv/.mamba/envs/MACH/external/petsc/include -I/home/andv/.mamba/envs/MACH/external/petsc/ -c communication.F90 -o ../../obj/communication.o

        --- Compiled communication.F90 successfully ---

mpifort -I../../mod -I/home/andv/.mamba/envs/MACH/external/cgns/include -I/home/andv/.mamba/envs/MACH/external/hdf5/include -fPIC -std=f2008 -fdefault-real-8 -O2 -I/home/andv/.mamba/envs/MACH/external/petsc/include -I/home/andv/.mamba/envs/MACH/external/petsc/ -c hypInput.f90 -o ../../obj/hypInput.o

        --- Compiled hypInput.f90 successfully ---

mpifort -I../../mod -I/home/andv/.mamba/envs/MACH/external/cgns/include -I/home/andv/.mamba/envs/MACH/external/hdf5/include -fPIC -std=f2008 -fdefault-real-8 -O2 -I/home/andv/.mamba/envs/MACH/external/petsc/include -I/home/andv/.mamba/envs/MACH/external/petsc/ -c hypData.F90 -o ../../obj/hypData.o
hypData.F90:4:6:

    4 |   use petsc
      |      1
Error: GNU Extension: Variable ‘petsc_comm_self’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
hypData.F90:4:6:

    4 |   use petsc
      |      1
Error: GNU Extension: Variable ‘petsc_comm_world’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
make[3]: *** [../../rulesSources.mk:19: hypData.o] Error 1
make[3]: Leaving directory '/home/andv/Downloads/MACH/pyhyp/src/modules'
make[2]: *** [Makefile:31: all] Error 2
make[2]: Leaving directory '/home/andv/Downloads/MACH/pyhyp/src/modules'
make[1]: *** [Makefile:46: hyp] Error 1
make[1]: Leaving directory '/home/andv/Downloads/MACH/pyhyp'
make: *** [Makefile:16: default] Error 2

Expected behavior

It should compile with default flags.

Code versions

  • Operating System: linux
  • Python: 3.9
  • OpenMPI: 4.1.2
  • CGNS: 4.2
  • PETSc: 3.15
  • This software:

unattachedEdgesAreSymmetry fails on some surface meshes

Type of issue

  • Bug

Description

The unattachedEdgesAreSymmetry option fails on certain surface meshes. When this fails, the volume mesh generated by pyHyp will have negative volumes along the symmetry plane. It is unclear why the failure occurs. Explicitly setting the symmetry boundary condition using the BC option is a possible workaround.

Extra surface BCs showing up in pointwise in PLOT3D file?

Hi,

Not sure if this is really an issue or support request, but I'm hoping that someone has come across this before!

The setup:

  • I use pointwise to generate a structured surface mesh, and export PLOT3D
  • I use pyhyp to extrude ~80-100 layers
  • Import volume mesh back into pointwise to set EXODUSII boundary conditions

I'm getting really nice extrusions on certain surface meshes, but in some specific cases, I see surface domains (that are selectable as BCs in pointwise) showing up at the interface between extrusion volumes (i.e. perpendicular to the wall). Is this expected? It seems to happen most at wing tips where there are wall surfaces that aren't tangent to one another?

Below is an example at a wing tip:

image

Ideally the only boundaries I would like to select are the initial wall surface mesh and the outer overset boundary. Is there something I'm doing in my surface mesh to cause a disconnect betwwen blocks? Or maybe this this just something that the pointwise import script is interpreting?

Apologies if this isn't really a pyhyp issue....

Exit gracefully in parallel

Description

When running pyHyp in parallel, it should exit gracefully using mpi_abort and exit code instead of plain stop, which will result in improper MPI exit. There are several locations where this needs to be fixed.

Segmentation fault

Hello. I'm trying to use pyhyp for a complex wing configuration. What could be causing this error: Segmentation fault? Quality mesh more the 0.7. What could be wrong? In what direction should I think? I use docker.

image
image

ERROR 7: VSPAERO Viewer Not Found.
        Expected here: /home/mdolabuser/packages/OpenVSP/python/openvsp/openvsp/vspviewer
#--------------------#
 Total Nodes:   36557
 Unique Nodes:  33713
 Total Faces:   33536
#--------------------#
 Normal orientation check ...
 Normals are consistent!
 Determining topology ...
 Topology complete.
#--------------------#
Grid Ratio:  1.7306
#--------------------#
#-------------------------------------------------------------------------------------------------------------------#
# Grid | CPU  | Sub | KSP | nAvg |  Sl  | Sensor | Sensor | Min     | Min     |  deltaS  | March    | cMax  | Ratio |
# Lvl  | Time | Its | Its |      |      | Max    | Min    | Quality | Volume  |          | Distance |       | kMax  |
#-------------------------------------------------------------------------------------------------------------------#
      2    0.3     2    14     61  0.019  1.00001  0.99989  0.03577  0.198E-16  0.100E-08  0.137E-08  0.0000  0.0000
      3    0.7     2    14     61  0.023  1.00002  0.99903  0.03552  0.368E-15  0.173E-08  0.410E-08  0.0000 24.5351
      4    0.8     1    14     61  0.024  1.00003  0.99840  0.03542  0.119E-14  0.299E-08  0.583E-08  0.0000  3.2697
      5    1.1     2    14     61  0.027  1.00005  0.99340  0.03539  0.386E-14  0.518E-08  0.140E-07  0.0000  3.2786
      6    1.4     2    14     61  0.030  1.00008  0.98651  0.03536  0.813E-14  0.897E-08  0.282E-07  0.0000  2.1136
      7    1.6     1    14     61  0.032  1.00012  0.97773  0.03532  0.171E-13  0.155E-07  0.371E-07  0.0000  2.1076
      8    1.9     2    14     61  0.035  1.00020  0.94985  0.03529  0.390E-13  0.269E-07  0.795E-07  0.0001  2.2893
      9    2.2     2    14     61  0.039  1.00035  0.90997  0.03525  0.752E-13  0.465E-07  0.153E-06  0.0002  1.9290
     10    2.4     1    13     61  0.041  1.00069  0.85486  0.03521  0.146E-12  0.805E-07  0.199E-06  0.0002  1.9409
     11    2.7     2    14     61  0.045  1.00202  0.73178  0.03516  0.298E-12  0.139E-06  0.419E-06  0.0007  2.0663
     12    3.0     2    14     61  0.050  1.00543  0.57029  0.03511  0.560E-12  0.241E-06  0.799E-06  0.0012  1.8683
     13    3.2     1    14     61  0.052  1.01237  0.40303  0.03505  0.104E-11  0.417E-06  0.104E-05  0.0012  1.8839
     14    3.5     2    15     61  0.058  1.03184  0.21303  0.03499  0.179E-11  0.722E-06  0.218E-05  0.0035  1.9798
     15    3.8     2    17     61  0.064  1.05095  0.11586  0.03493  0.317E-11  0.125E-05  0.415E-05  0.0061  1.8327
     16    4.0     1    17     61  0.067  1.06841  0.10000  0.03485  0.537E-11  0.216E-05  0.540E-05  0.0061  1.8399
     17    4.4     2    30     61  0.075  1.08002  0.10000 -0.01915  0.913E-11  0.374E-05  0.113E-04  0.0180  1.9021
     18    4.9     2    40     61  0.082  1.22213  0.10000 -0.02140  0.185E-10  0.647E-05  0.215E-04  0.0307  1.7985
     19    5.2     1    31     61  0.085  5.08805  0.10000  0.03460  0.359E-10  0.112E-04  0.280E-04  0.0304  1.9837
     20    6.3     2    92     62  0.095 ********  0.10000 -1.00000 -0.711E-04  0.194E-04  0.586E-04  0.0977 *******
     21    6.6     2    22    110  0.105 ********  0.10000 -1.00000 -0.105E+01  0.335E-04  0.112E-03  0.1902 *******
     22   15.3     1  1500    164  0.109 ********  0.10000 -1.00000 -0.756E+18  0.581E-04  0.145E-03  0.1370 *******
     23   15.5     2     0  33709  0.118  0.10000  0.10000      NaN        NaN  0.100E-03  0.239E-03     NaN     Inf
     24   15.6     2     0  33709  0.132  0.10000  0.10000      NaN        NaN  0.174E-03  0.513E-03     NaN  0.0000
     25   15.7     2     0  33709  0.146  0.10000  0.10000      NaN        NaN  0.301E-03  0.988E-03     NaN  0.0000
     26   15.8     1     0  33709  0.152  0.10000  0.10000      NaN        NaN  0.521E-03  0.129E-02     NaN  0.0000
     27   15.9     2     0  33709  0.170  0.10000  0.10000      NaN        NaN  0.901E-03  0.271E-02     NaN  0.0000
     28   16.0     2     0  33709  0.187  0.10000  0.10000      NaN        NaN  0.156E-02  0.517E-02     NaN  0.0000
     29   16.1     1     0  33709  0.194  0.10000  0.10000      NaN        NaN  0.270E-02  0.673E-02     NaN  0.0000
     30   16.2     2     0  33709  0.217  0.10000  0.10000      NaN        NaN  0.467E-02  0.141E-01     NaN  0.0000
     31   16.4     2     0  33709  0.239  0.10000  0.10000      NaN        NaN  0.808E-02  0.269E-01     NaN  0.0000
     32   16.4     1     0  33709  0.249  0.10000  0.10000      NaN        NaN  0.140E-01  0.349E-01     NaN  0.0000
     33   16.6     2     0  33709  0.278  0.10000  0.10000      NaN        NaN  0.242E-01  0.731E-01     NaN  0.0000
     34   16.7     2     0  33709  0.306  0.10000  0.10000      NaN        NaN  0.419E-01  0.139E+00     NaN  0.0000
     35   16.7     1     0  33709  0.319  0.10000  0.10000      NaN        NaN  0.725E-01  0.181E+00     NaN  0.0000
     36   16.9     2     0  33709  0.356  0.10000  0.10000      NaN        NaN  0.125E+00  0.379E+00     NaN  0.0000
     37   17.0     2     0  33709  0.392  0.10000  0.10000      NaN        NaN  0.217E+00  0.722E+00     NaN  0.0000
     38   17.0     1     0  33709  0.408  0.10000  0.10000      NaN        NaN  0.376E+00  0.939E+00     NaN  0.0000
     39   17.2     2     0  33709  0.456  0.10000  0.10000      NaN        NaN  0.650E+00  0.197E+01     NaN  0.0000
     40   17.3     2     0  33709  0.502  0.10000  0.10000      NaN        NaN  0.113E+01  0.374E+01     NaN  0.0000
     41   17.3     1     0  33709  0.522  0.10000  0.10000      NaN        NaN  0.195E+01  0.487E+01     NaN  0.0000
     42   17.5     2     0  33709  0.583  0.10000  0.10000      NaN        NaN  0.337E+01  0.102E+02     NaN  0.0000
     43   17.6     2     0  33709  0.642  0.10000  0.10000      NaN        NaN  0.583E+01  0.194E+02     NaN  0.0000
     44   17.6     1     0  33709  0.668  0.10000  0.10000      NaN        NaN  0.101E+02  0.252E+02     NaN  0.0000
     45   17.8     2     0  33709  0.746  0.10000  0.10000      NaN        NaN  0.175E+02  0.528E+02     NaN  0.0000
     46   17.9     2     0  33709  0.822  0.10000  0.10000      NaN        NaN  0.302E+02  0.100E+03     NaN  0.0000
     47   18.0     1     0  33709  0.855  0.10000  0.10000      NaN        NaN  0.523E+02  0.131E+03     NaN  0.0000
     48   18.1     2     0  33709  0.955  0.10000  0.10000      NaN        NaN  0.906E+02  0.274E+03     NaN  0.0000
     49   18.2     2     0  33709  1.052  0.10000  0.10000      NaN        NaN  0.157E+03  0.521E+03     NaN  0.0000
Segmentation fault

pyHyp doesn't work with numpy 1.24

Description

Self explanatory. We are trying to update the "latest" docker images to numpy 1.24 (https://github.com/mdolab/docker/pull/208) and getting the error below in all the pyHyp tests. This error looks pretty much identical to mdolab/adflow#256 so the solution will likely also be similar

Steps to reproduce issue

  1. Install numpy v1.24
  2. Run pyHyp tests

Current behavior

2023-01-17T17:05:27.9879234Z (mpi) ./test_all_examples.py:TestExamples.test_sphere ... FAIL (00:00:0.94, 315 MB)
2023-01-17T17:05:27.9880090Z Traceback (most recent call last):
2023-01-17T17:05:27.9881809Z   File "/home/***/.pyenv/versions/3.10.9/lib/python3.10/site-packages/testflo/test.py", line 418, in _try_call
2023-01-17T17:05:27.9886788Z     func()
2023-01-17T17:05:27.9887811Z   File "/home/***/repos/pyhyp/tests/./test_all_examples.py", line 98, in test_sphere
2023-01-17T17:05:27.9888961Z     from examples.sphere.runSphere import volumeFile, commonOptions
2023-01-17T17:05:27.9889972Z   File "/home/***/repos/pyhyp/tests/../examples/sphere/runSphere.py", line 55, in <module>
2023-01-17T17:05:27.9891336Z     hyp = pyHypMulti(options=options, commonOptions=commonOptions, skipList=skipList)
2023-01-17T17:05:27.9892759Z   File "/home/***/repos/pyhyp/tests/../pyhyp/pyHyp.py", line 225, in __init__
2023-01-17T17:05:27.9893807Z     hypGrid = pyHyp(comm, options, debug)
2023-01-17T17:05:27.9895165Z   File "/home/***/repos/pyhyp/tests/../pyhyp/pyHyp.py", line 424, in __init__
2023-01-17T17:05:27.9895976Z     self._setOptions()
2023-01-17T17:05:27.9896977Z   File "/home/***/repos/pyhyp/tests/../pyhyp/pyHyp.py", line 763, in _setOptions
2023-01-17T17:05:27.9898101Z     self.hyp.hypinput.sourcestrengthfile = self._expandString("")
2023-01-17T17:05:27.9899552Z ValueError: 0-th dimension must be 512 but got 0 (not defined).

Expected behavior

All tests pass

Problem about PyHyp install

Thanks for your codes.

I install it follow the file "index.rst",but I meet a problem.

I run the command 'make', and it reports

"Error: hyp.so was not imported correctly"

After that, I run comand ‘import hyp.so’ in python, it reports

"ImportError: libcgns.so.3.1: cannot open shared object file: No such file or directory"

But the fie 'libcgns.so.3.1' exists and I already add its path in config.mk.

I hope you can help me, thank you.

Improve testing coverage

We need to improve testing coverage, both in terms of unit and regression tests. Currently, we only run regression tests using the examples found in the examples directory. Furthermore, these test are limited in scope as they only cover block size and topology. Changes in BCs and coordinates are not captured in the current tests.

Naming BC in pyhyp

I am currently running the 2D naca0012 tutorial in pyhyp. Everything works well. However, I need to specify names to the airfoil surface as well as the farfield domain in order to be able to specify boundary conditions to these surfaces in SU2. How do I do this?

Error when generating pyhyp mesh - "Segmentation fault (core dumped)"

Dear all,

I am trying to generate a Mesh around a 2D airfoil using pyhyp. Find attached the genMesh.py file. When running the mesh, the error "Segmentation fault (core dumped)" appears, and if I then try to run the CFDrun.py with that mesh, the following message appears:

                      Warning
 It is assumed that the grid is given in meters.


 Specified load imbalance tolerance  0.100 acheived
 Continuing with  0.000 load imbalance for the cells and  0.000 for the faces


 Found 2 blocks for which the boundary or connectivity information
 is not correct. Here is the list of bad blocks

 Zone domain.00001: iMin block face not fully described
 Zone domain.00001: iMax block face not fully described

--------------------------- !!! Error !!! ----------------------------
* Terminate called by processor 0
* Run-time error in procedure checkFaces
* Error message: Wrong block boundary info found
*
* Now exiting
----------------------------------------------------------------------

I tried to open the cgns file on Paraview, but since the error comes before the mesh is finished, I cannot visualize the mesh and therefore cannot find where the error might be. Can someone help me please? Attached the airfoil .dat file and the genMesh.py
26_max_CLCD.txt
genMesh.txt

Mismatched config filename in compilation step of installation instructions

Filename

What types of issue is it?

  • Documentation update

Description

In the instructions in this link: https://mdolab-pyhyp.readthedocs-hosted.com/en/latest/install.html, it says to copy a file named config.LINUX_GFORTRAN.mk
but the only files in the config/defaults/ are
config.LINUX_GFORTRAN_OPENMPI.mk
and
config.LINUX_INTEL_OPENMPI.mk
Is there supposed to be a file named
config.LINUX_GFORTRAN.mk
in there or is this just a documentation update? I am unsure so I didn't want to submit a pull request.

Steps to reproduce issue

  1. …N/A

Current behavior

Expected behavior

Code version (if relevant)

Python version:

External dependencies:

Internal packages:

problem reading exports from GMSH

Edit: I will try to compile GMSH from source on the mdolab image and let you know

I am trying to read multi-block grid generatey by GMSH version 4.12.2 but somehow it fails.

The code to generate the surface is:

lc = 100;
cx = 324925.0;
cy = 5216025.0;
s = 3000.0;
r = 16000.0;


// Number of cells at inner square
Ns = 12;
// Number of cells between inner square and circle
Ni = 36;




// Horizontal gradings
blockGradi = 1.1;
blockGrads =  1.0;

// Inner square side curvature - 0.4
scr = 1.1;
sc = s * scr;


// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //


// 45 degree points angle
a0 = -45;
a1 = -135;
a2 = 135;
a3 = 45;

// Half of 45 degree points angle
ea0 = 0;
ea1 = -90;
ea2 = 180;
ea3 = 90;

ca0 = Cos((Pi/180)*a0);
ca1 = Cos((Pi/180)*a1);
ca2 = Cos((Pi/180)*a2);
ca3 = Cos((Pi/180)*a3);

sa0 = Sin((Pi/180)*a0);
sa1 = Sin((Pi/180)*a1);
sa2 = Sin((Pi/180)*a2);
sa3 = Sin((Pi/180)*a3);

cea0 = Cos((Pi/180)*ea0);
cea1 = Cos((Pi/180)*ea1);
cea2 = Cos((Pi/180)*ea2);
cea3 = Cos((Pi/180)*ea3);

sea0 = Sin((Pi/180)*ea0);
sea1 = Sin((Pi/180)*ea1);
sea2 = Sin((Pi/180)*ea2);
sea3 = Sin((Pi/180)*ea3);

// Inner square x and y position

Point(1) = {cx, cy, 0, lc};


Point(11) = {cx-s, cy-s, 0, lc};
Point(12) = {cx-s, cy+s, 0, lc};
Point(13) = {cx+s, cy+s, 0, lc};
Point(14) = {cx+s, cy-s, 0, lc};


Point(21) = {cx+r*ca1, cy+r*sa1, 0, lc};
Point(22) = {cx+r*ca2, cy+r*sa2, 0, lc};
Point(23) = {cx+r*ca3, cy+r*sa3, 0, lc};
Point(24) = {cx+r*ca0, cy+r*sa0, 0, lc};


Point(31) = {cx-sc, cy, 0, lc};
Point(32) = {cx, cy+sc, 0, lc};
Point(33) = {cx+sc, cy, 0, lc};
Point(34) = {cx, cy-sc, 0, lc};


Circle(1) = {21, 1, 22};
Circle(2) = {22, 1, 23};
Circle(3) = {23, 1, 24};
Circle(4) = {24, 1, 21};



// Gmsh provides other curve primitives than stright lines: splines,
// B-splines, circle arcs, ellipse arcs, etc. Here we define a new
// circle arc, starting at point 14 and ending at point 16, with the
// circle's center being the point 15:

Spline(21) = {11,31,12};
Spline(22) = {12,32,13};
Spline(23) = {13,33,14};
Spline(24) = {14,34,11};


Line(31) = {11, 21};
Line(32) = {12, 22};
Line(33) = {13, 23};
Line(34) = {14, 24};


Curve Loop(1) = {21, 22, 23, 24};
Surface(1) = {1};

Curve Loop(11) = {1, -32, -21, 31};
Surface(11) = {11};

Curve Loop(12) = {32, 2, -33, -22};
Surface(12) = {12};

Curve Loop(13) = {33, 3, -34, -23};
Surface(13) = {13};

Curve Loop(14) = {34, 4, -31, -24};
Surface(14) = {14};


Transfinite Curve {1, 2, 3, 4} = Ni+1 Using Progression 1.0;
Transfinite Curve {21, 22, 23, 24} = Ni+1 Using Progression 1.0;
Transfinite Curve {31, 32,33,34} = Ns+1 Using Progression blockGradi;


Transfinite Surface {1} = {11, 12, 13, 14};
Transfinite Surface {11} = {21, 22, 12, 11};
Transfinite Surface {12} = {22, 23, 13, 12};
Transfinite Surface {13} = {23, 24, 14, 13};
Transfinite Surface {14} = {24, 21, 11, 14};


Recombine Surface {1, 11, 12, 13, 14};

Physical Curve("LEFT") = {1};
Physical Curve("TOP") = {2};
Physical Curve("RIGHT") = {3};
Physical Curve("BOTTOM") = {4};
Physical Surface("TERRAIN1") = {1};
Physical Surface("TERRAIN2") = {11};
Physical Surface("TERRAIN3") = {12};
Physical Surface("TERRAIN4") = {13};
Physical Surface("TERRAIN5") = {14};


Mesh 2;

Mesh.Smoothing = 0;
Mesh.RecombineAll = 1;
Mesh.Smoothing = 0;


Mesh.CgnsExportStructured = 1;
Mesh.Format = 32;	//CGNS fails
// Mesh.Format = 28;	//P3D

So I export the data using the PLOT3D Driver, and pyhyp can load it. Somehow, the normals are inverted, but I can live with it.
Now, Paraview 5.11.2 can read the CGNS output generated by GMSH (Mesh.Format = 32). So I would like to do a bit of processing, show below, modify the output of GMSH, and save it to VTM and then CGNS from paraview.

baseDir = os.path.dirname(os.path.abspath(__file__))
surfaceFile = os.path.join(baseDir, "circular_domain.p3d")
print(surfaceFile)
assert os.path.isfile(surfaceFile), surfaceFile



elevFile = os.path.join(baseDir, "grossglockner_elevation_data.vts")
print(elevFile)
assert os.path.isfile(elevFile), elevFile

import vtk
from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk

dem_reader = vtk.vtkXMLStructuredGridReader()
dem_reader.SetFileName(elevFile)
dem_reader.Update()
dem = dem_reader.GetOutput()
dem_pts = vtk_to_numpy(dem.GetPoints().GetData())
dem_pts[:, 2] = 0
pts = vtk.vtkPoints()
pts.SetData(numpy_to_vtk(dem_pts))
dem.SetPoints(pts)


if 1:   
    reader = vtk.vtkCGNSReader()
    reader.SetFileName("circular_domain.cgns")
    reader.Update()

    _org = reader.GetOutput()
    out = _org.GetBlock(0)
    for b in range(out.GetNumberOfBlocks()):
        block = out.GetBlock(b)
        pdata = vtk.vtkPolyData()
        pdata.SetPoints(block.GetPoints())
        # print(pdata.GetPoints().GetNumberOfPoints())
        probeFilter = vtk.vtkProbeFilter()
        probeFilter.SetInputData(pdata)
        probeFilter.SetSourceData(dem)
        probeFilter.Update()
        z = vtk_to_numpy(probeFilter.GetOutput().GetPointData().GetArray("Elevation"))
        print((z.min(), z.max()))
        pts3d = vtk_to_numpy(block.GetPoints().GetData())
        pts3d[:, 2] = -z
        pts = vtk.vtkPoints()
        pts.SetData(numpy_to_vtk(pts3d))
        block.SetPoints(pts)
    writer = vtk.vtkXMLMultiBlockDataWriter()
    writer.SetFileName("circular_domain_scaled.vtm")
    writer.SetInputData(_org)
    writer.Update()

# Wish i could save from VTK to CGNS
# But the we can load it in Paraview and re-export as CGNS

    

options = {

    # ---------------------------
    "inputFile": surfaceFile,
    "fileType": "PLOT3D",
    "unattachedEdgesAreSymmetry": False,
    "outerFaceBC": "farfield",
    "autoConnect": True,

...

but somehow, the file is still corrupted. Any idea where this comes from?

image

This is what my CGNS looks like in Paraview

image

I must point out that I am running it in a container and that the files are written on a CIFS volume. I will try to write them under '/tmp', maybe this could be help.

Thanks

Volume mesh generation of complex configurations

Can this tool be used to generate the volume mesh of the wing-body or wing-body-tail configurations automatically based on relative high quality surface mesh? If it works, How do I set the parameters?Thanks!

volume mesh generation in pHYP

I'm trying to generate volume mesh for wing+body using pyHYP .I'm able to run pyhyp script without errors,but the grid is only generating for some distance instead of given march distance. this is the script

from pyhyp import pyHyp

options = {
    # ---------------------------
    #   General options
    # ---------------------------
    "inputFile": "wb_1.6ar_0.67s.cgns",
    "fileType": "CGNS",
    "unattachedEdgesAreSymmetry": False,
    "outerFaceBC": "farfield",
    "autoConnect": True,
    "BC": {1: {"iHigh": "zSymm"},5: {"jLow": "zSymm"},6: {"jHigh": "zSymm"},7: {"jHigh": "zSymm"},8: {"jLow": "zSymm"},9: {"jLow": "zSymm"},10: {"jLow": "zSymm"},11: {"iHigh": "zSymm"},12: {"jHigh": "zSymm"},14: {"iHigh": "zSymm"}, 15: {"iHigh": "zSymm"}, 17: {"iLow": "zSymm","iHigh": "zSymm"},25: {"jLow": "zSymm"},26: {"jLow": "zSymm"},27: {"jHigh": "zSymm"}},
    
    "families": "wall",

    # ---------------------------
    #   Grid Parameters
    # ---------------------------
    "N":129,
    "s0": 1e-6,
    "marchDist" : 22.5,
    "nConstantStart":100,
    
   
    # ---------------------------
    #   Pseudo Grid Parameters
    # ---------------------------
    "ps0": -1.0,
    "pGridRatio":-1.0,
    "cMax":1.0,
   
    # ---------------------------
    #   Smoothing parameters
    # ---------------------------
    "epsE": 3.0,
    "epsI": 6.0,
    "theta": 3.0,
    "volCoef": 0.15,
    "volBlend": 0.0005,
    "volSmoothIter": 100,
    "volSmoothSchedule": [[0, 10], [0.4, 50], [1.0, 100]],
    "slExp":0.073,
  
    # ---------------------------
    #   Solution Parameters
    # ---------------------------
    "kspRelTol": 1e-10,
    "kspMaxIts": 1500,
    "kspSubspaceSize": 120,
    "writeMetrics":True,
}

hyp = pyHyp(options=options)
hyp.run()
hyp.writeCGNS("wb_vol.cgns")

what changes can avoid this.Thanks in advance

Compling problems with new version of petsc

Type of issue

What types of issue is it?

  • Other (code version incompatible)

Description

Incompatibilities with the latest version of petsc.

Steps to reproduce issue

  1. Use the latest version of petsc, 3.11.3, and compiling it with the select option:
    ./configure
    --with-shared-libraries
    --with-fortran-interfaces=1
    --with-scalar-type=real
    --PETSC_ARCH=real-gfortran-opt-3.11.3
    --with-debugging=no
    --with-cc=gcc
    --with-cxx=g++
    --with-fc=gfortran
    --with-cxx-dialect=C++11
    --prefix=/home/guardmdo/apps/petsc-real-opt-3113
    --download-fblaslapack=yes
    --download-metis=yes
    --download-parmetis=yes
    --download-superlu_dist=yes
    --download-openmpi=yes
    --download-mpi4py=yes
    --download-petsc4py=yes

  2. Compiling the pyhyp with the following commands:
    make

  3. Compiling failed

Current behavior

The failed infomation :

mpif90 -I../../mod -I/home/guardmdo/apps/cgnslib-3.2.1/include   -fPIC -fPIC -fdefault-real-8 -O2 -I/home/guardmdo/apps/petsc-real-opt-3113/include -I/home/guardmdo/apps/petsc-real-opt-3113 -c hypData.F90 -o ../../obj/hypData.o
hypData.F90:8:2:

 #else
  1~~~~                        
**Fatal Error: petsc/finclude/petscvec.h90: No such file or directory**
compilation terminated.

Expected behavior

I try to search the petsc updating history in the
https://github.com/petsc/petsc.git
and find that:
In recent two years, the released versions of petsc seem to remove *.h90 files to other places and delete some *.h90 files, and these files are no longer in the path "petsc/finclude/"

So, brothers, do your have plans to update the code to fit the new version of petsc? like the latest version petsc-3.11.3?

Code version (if relevant)

Python version: 2.7.15+

External dependencies: GCC 7.3.0

Internal packages: PETSc 3.11.3

Document the BC option

Type of issue

  • Documentation update

Description

The BC option is currently undocumented.

The documentation should be updated to include:

  • A description of the BC option in the options table
  • Instructions on how to identify the block index and edge specification
  • A warning that unattachedEdgesAreSymmetry may fail for some surface meshes and to try the BC option (#26)

Which version of HDF5

Description

When I run testflo -v or run an example such as examples/m6/runM6.py, it returns an error about HDF5.

Should I build an HDF5-1.8.23 instead? Or shall I re-make pyhyp?

Thank you.

Current behavior

        Warning! ***HDF5 library version mismatched error***
        The HDF5 header files used to compile this application do not match
        the version used by the HDF5 library to which this application is linked.
        Data corruption or segmentation faults may occur if the application continues.
        This can happen when an application was compiled by one version of HDF5 but
        linked with a different version of static or shared HDF5 library.
        You should recompile the application or check your shared library related
        settings such as 'LD_LIBRARY_PATH'.
        You can, at your own risk, disable this warning by setting the environment
        variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
        Setting it to 2 or higher will suppress the warning messages totally.
        Headers are 1.8.23, library is 1.10.7
        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

        General Information:
        -------------------
               HDF5 Version: 1.10.7
              Configured on: Wed, 08 Dec 2021 23:33:27 +0000
              Configured by: Debian
                Host system: x86_64-pc-linux-gnu
          Uname information: Debian
                   Byte sex: little-endian
         Installation point: /usr
                Flavor name: serial

        Compiling Options:
        ------------------
                 Build Mode: production
          Debugging Symbols: no
                    Asserts: no
                  Profiling: no
         Optimization Level: high

        Linking Options:
        ----------------
                  Libraries: static, shared
        Statically Linked Executables:
                    LDFLAGS: -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro
                 H5_LDFLAGS: -Wl,--version-script,$(top_srcdir)/debian/map_serial.ver
                 AM_LDFLAGS:
            Extra libraries: -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm
                   Archiver: ar
                   AR_FLAGS: cr
                     Ranlib: x86_64-linux-gnu-ranlib

        Languages:
        ----------
                          C: yes
                 C Compiler: /usr/bin/gcc
                   CPPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2
                H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                AM_CPPFLAGS:
                    C Flags: -g -O2 -ffile-prefix-map=$(top_srcdir)=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
                 H5 C Flags:  -std=c99  -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-c++-compat -Wno-format-nonliteral -Wshadow -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3  -Werror=bad-function-cast -Werror=declaration-after-statement -Werror=implicit-function-declaration -Werror=missing-declarations -Werror=missing-prototypes -Werror=nested-externs -Werror=old-style-definition -Werror=packed -Werror=pointer-sign -Werror=pointer-to-int-cast -Werror=redundant-decls -Werror=strict-prototypes -Werror=switch -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wunused-but-set-variable -Wformat -Werror=incompatible-pointer-types -Werror=shadow -Wcast-function-type -Wmaybe-uninitialized
                 AM C Flags:
           Shared C Library: yes
           Static C Library: yes


                    Fortran: yes
           Fortran Compiler: /usr/bin/gfortran
              Fortran Flags: -g -O2 -ffile-prefix-map=$(top_srcdir)=. -flto=auto -ffat-lto-objects -fstack-protector-strong
           H5 Fortran Flags:  -std=f2008  -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Wuse-without-only -Winteger-division -Wfrontend-loop-interchange  -s -O3
           AM Fortran Flags:
     Shared Fortran Library: yes
     Static Fortran Library: yes

                        C++: yes
               C++ Compiler: /usr/bin/g++
                  C++ Flags: -g -O2 -ffile-prefix-map=$(top_srcdir)=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
               H5 C++ Flags:   -Wall -Wcast-qual -Wconversion -Wctor-dtor-privacy -Weffc++ -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-format-nonliteral -Wnon-virtual-dtor -Wold-style-cast -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -O3  -Wcast-align -Wmissing-declarations -Werror=packed -Werror=redundant-decls -Werror=switch -Wunused-but-set-variable -Werror=unused-function -Werror=unused-variable -Wunused-parameter -Werror=shadow
               AM C++ Flags:
         Shared C++ Library: yes
         Static C++ Library: yes

                       Java: yes
              Java Compiler: /usr/bin/java (openjdk 11.0.13 2021-10-19)


        Features:
        ---------
               Parallel HDF5: no
        Parallel Filtered Dataset Writes: no
          Large Parallel I/O: no
          High-level library: yes
            Build HDF5 Tests: yes
            Build HDF5 Tools: yes
                Threadsafety: yes
         Default API mapping: v18
        With deprecated public symbols: yes
      I/O filters (external): deflate(zlib),szip(encoder)
                         MPE: no
                  Direct VFD: no
                  Mirror VFD: no
          (Read-Only) S3 VFD: yes
        (Read-Only) HDFS VFD: no
                     dmalloc: no
        Packages w/ extra debug output: none
                 API tracing: no
        Using memory checker: no
        Memory allocation sanity checks: no
      Function stack tracing: no
            Use file locking: best-effort
        Strict file format checks: no
        Optimization instrumentation: no
        Bye...

        [WSL:05487] *** Process received signal ***
        [WSL:05487] Signal: Aborted (6)
        [WSL:05487] Signal code:  (-6)
        [WSL:05487] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7fa0bf3a3520]
        [WSL:05487] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7fa0bf3f7a7c]
        [WSL:05487] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7fa0bf3a3476]
        [WSL:05487] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7fa0bf3897f3]
        [WSL:05487] [ 4] /lib/x86_64-linux-gnu/libhdf5_serial.so.103(+0x3d49a)[0x7fa0a4ca849a]
        [WSL:05487] [ 5] /home/lrz/opt/CGNS-4.3.0/opt-gfortran/lib/libcgns.so.4.3(ADFH_Database_Open+0x635)[0x7fa0a50a86e5]
        [WSL:05487] [ 6] /home/lrz/opt/CGNS-4.3.0/opt-gfortran/lib/libcgns.so.4.3(cgio_open_file+0x269)[0x7fa0a505eaa9]
        [WSL:05487] [ 7] /home/lrz/opt/CGNS-4.3.0/opt-gfortran/lib/libcgns.so.4.3(cg_open+0x98)[0x7fa0a5062b58]
        [WSL:05487] [ 8] /home/lrz/opt/CGNS-4.3.0/opt-gfortran/lib/libcgns.so.4.3(cg_open_f_+0x1af)[0x7fa0a50ae64f]
        [WSL:05487] [ 9] /tmp/tmpsj_1f9c4/hyp.so(writecgns_+0x166e)[0x7fa0a456fcfe]
        [WSL:05487] [10] /tmp/tmpsj_1f9c4/hyp.so(+0x10c7b)[0x7fa0a4545c7b]
        [WSL:05487] [11] python(_PyObject_MakeTpCall+0x158)[0x559b367cfda8]
        [WSL:05487] [12] python(_PyEval_EvalFrameDefault+0x4448)[0x559b3682e6f8]
        [WSL:05487] [13] python(_PyFunction_Vectorcall+0x108)[0x559b367fc768]
        [WSL:05487] [14] python(+0x146254)[0x559b367aa254]
        [WSL:05487] [15] python(_PyEval_EvalCodeWithName+0x1e9)[0x559b367fb9c9]
        [WSL:05487] [16] python(PyEval_EvalCode+0x23)[0x559b3685b383]
        [WSL:05487] [17] python(+0x1f78d2)[0x559b3685b8d2]
        [WSL:05487] [18] python(+0x207982)[0x559b3686b982]
        [WSL:05487] [19] python(+0x209429)[0x559b3686d429]
        [WSL:05487] [20] python(PyRun_SimpleFileExFlags+0x1bf)[0x559b3686d60f]
        [WSL:05487] [21] python(Py_RunMain+0x2f9)[0x559b3686da09]
        [WSL:05487] [22] python(Py_BytesMain+0x39)[0x559b3686dca9]
        [WSL:05487] [23] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7fa0bf38ad90]
        [WSL:05487] [24] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7fa0bf38ae40]
        [WSL:05487] [25] python(+0x1e21c7)[0x559b368461c7]
        [WSL:05487] *** End of error message ***
        Aborted

Code versions

  • Operating System: Ubuntu.22.04.02
  • Python: 3.9
  • OpenMPI: openmpi-4.1.4
  • CGNS: CGNS-4.3.0
  • PETSc: petsc-3.18.2
  • Compiler: gfortran 11.3.0
  • HDF5: 1.10.7

Add a theory section in the documentation

Type of issue

  • Documentation update

Description

The descriptions in the options table refer to a non-existent theory section several times. A theory section should be added to the documentation.

Compile Error

Description

When make, returns error:

readCGNS.F90:177:99:

177 | call cg_goto_f(cg, base, ierr, "Zone_t", iBlock, "ZoneBC_t", 1, "BC_t", iBC, "end")
| 1

Error: More actual than formal arguments in procedure call at (1)

Code versions

  • Operating System: Ubuntu.22.04.02
  • Python: 3.9
  • OpenMPI: openmpi-4.1.4
  • CGNS: CGNS-4.3.0 or CGNS-4.1.2
  • PETSc: petsc-3.18.2
  • Compiler: gfortran 11.3.0
  • This repository:

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